*

Molecule files

*

MOL2MOL can automatically recognize (R) and write (W) the following molecule file formats:

 

True modelling program files:

ALCHEMY I-III (Tripos Associates, Inc.) *RW M
SYBYL mol -"- *RW M
SYBYL mol2 -"- *RW M
MDL mol ver 2, 3
MDL reaction
(MDL Information Systems Inc.) *RW
*R
M
MDL SD
MDL RD
(MDL Information Systems Inc.) *RW
*R
M
CSSR (Daresbury Laboratory) *RW M
Desktop Molecular Modeller (Polyhedron Software) *RW M
PCModel (Serena Software) *RW M
HyperChem hin (HyperCube Inc) *RW M
HyperChem hcs   *R M
MOBY (Springer) *RW M
Insight car (Biosym) *RW M
MacroModel (Schrödinger L.L.C.) *RW M
Maestro (Schrödinger L.L.C.) *RW M
Tinker (J. W. Ponder) *R M
CAChe (Oxford Molecular) *RW M
CACAO car (C. Mealli, D.M.Proserpio) *RW M
Xmol and Unichem xyz (Research Equipment Inc.) *RW M
MXYZ *RW M
Brookhaven PDB
   (official, PDBQ, Rasmol/Chime, PDBFat)
(Brookhaven PDB) *RW M
ChemDraft (C_Graph Software) *RW M
Molecules-3D (Chemical Arts Corp.) *RW M
Beilstein Rosdal (Softron) *R M
MOPLO (VCH) *RW M
Z-matrix
   general and user defined free format
   MOPAC, AMPAC
   Gaussian type
 
#RW
 RW
 RW
 
U
U
Cartesian general free format #RW U
Gaussian 98 and 03 and Gamess output files #R M
Q-Chem input file (Q-Chem, Inc.) *RW M
Gamess input file (Gordon Research Group, Iowa State Uni.) *RW M
Turbomol input and output files (COSMOlogic GmbH) *R M
X-ray fractional
   SHELX
   CIF CIF/MIF
   Cambridge FDAT
   Cambridge Model
   free format
*RW
*RW
*R
*R
RW
C
C
C
C
C
User defined free format   *RW U

 

Drawing or plotting program files:

PLUTO (CSD and PC versions) W
WinPLT (H. G. Reich) W
WIMP (Aldrich Chemical Co.) W
SCHAKAL (Univ. Freiburg) W
DrawIt(ChemWindow) mol (Sadtler) *RW M
UltraMol (formerly MolPick) (CompuChem) *RW M
ChemDraw CT (Cambridge Sci. Comp. Inc.) *RW M
POV-Ray (POV-Ray Team) W  
Mol2Mol (T.E. Gunda *RW U

* Recognized automatically
# The insertion of a marker is necessary, if reading the file.
The letters M C and U show the File input option to be selected (see molecule files)

The conversion is performed automatically, but because different programs may use different special atom or bond types (extended atoms, dummy atoms, lone electron pairs, aromatic bonds or atoms etc), Mol2Mol may sometimes prompt you for additional information. A brief summary of the atom and bond types used by the different programs can be found under the a ppropriate headings.

Some modelling programs require the use of a specific extension to the file name for their coordinate files (e.g. .MOL or .DAT). In such cases Mol2Mol may add the extension automatically, if it has not been specified.


ALCHEMY and SYBYL  (read & write) *

On using an old ALCHEMY I-II file, dummy atoms are assigned to unknown or user-defined atom types. In addition to the standard types, ALCHEMY III and SYBYL can accommodate many atom types (all elements are allowed). You can select one of the two file types used by SYBYL, mol or mol2. SYBYL mol2 files may contain additional information, but Mol2Mol only interprets the structural atom, bond and fragment (e.g. amino acid moieties) information. If a Sybyl mol2 file comprises more than one molecule, you can choose whether the whole structure is loaded or only a part of it.

On writing on ALCHEMY file, Mol2Mol defaults to the ALCHEMY III file formats. This can be changed in the Preferences. In the case of old versions I or II the atom charge data (if any) are not written into the file and all non-standard elements (mostly metals) are changed to dummy atoms.

Files of Sybyl mol2 format may contain residue, chain and model information in the case of biopolymers. Mol2Mol will regard such a file to a "genuine" PDB-compatible one, if it contains at least one standard residue name. If so, a green letter PDB will lit in the upper status bar. In this case residue etc info will be passed to new PDB, HyperChem, Insight and MacroModel files (and vice versa).

If the original creator program is HyperChem, aromatic bonds are erroneously assigned to amide bonds when saving in Sybyl mol2 file format. Such HyperChem produced mol2 files can be automatically corrected in Mol2Mol.

Sometimes the sequence of the atoms is jumbled in the file: it is not in compliance with the residues or chains. In this case Mol2Mol rearranges the atoms.

Bond types:

Alchemy: SINGLE, DOUBLE, TRIPLE, AMIDE, AROMATIC
Sybyl mol: 1, 2, 3, 4 (amide), 5 (aromatic), 8 (dummy)
Sybyl mol2: 1,2,3, ar, am
Standard atom types:

AlchemySybyl molSybyl mol2
H13H hydrogen
H13H.t3p water TIP3P hydrogen
H13H.spc water TIP3P hydrogen
etc...

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MDL mol   (read & write)
(ISIS/Draw, ISIS/Base, old CPSS/ChemText, ChemBase, MACCS, REACCS etc),
MDL rxn   (read)
(ISIS/Draw, ISIS/Base, REACCS)
*

Apart from MDL's own programs, this molfile format is used by several other programs (ChemDraw, ChemX, ChemWindow etc). Sometimes Mol2Mol may have difficulty reading MDL molecule files created by other MDL or third-party programs if they contain a non-standard header. Although Mol2Mol tries to parse the file by several criteria, it may produce an "Unknown molfile" error message. In this case simply select the MDL mol entry in the Manual mode list box of the Open file dialog window or see the instructions for details on how to edit the header…

ISIS/Draw is capable of 3D rotation. Mol2Mol can therefore be used to import complex stereo structures into documents. Up, down and either stereo bonds from other files will be preserved. Structural descriptors, S-groups, 3D-features and other similar features are neglected, group abbreviations (superatoms) are expanded. If a 2D MDL file is in the workplace, implicit hydrogens are added. The same rules are applied as in ISIS/Draw. Moreover if the file contains atom aliases, these will be also shown.

Aromatic bonds are not supported by simple MDL files, only in query structures, or in drawings as dotted lines. Thus, on converting a molfile with aromatic bonds or atoms to this format, the program prompts you to convert them either to alternating single and double bonds, or to "dotted" bonds.

The new V3000 version is also supported.

MDL molfiles can be outputted as a javascript variable for the use as an inline structure in the Jmol browser applet. Select the as JMOL variable radio button from the Save file dialog window.

MDL programs can copy and paste molecules to the Windows clipboard in a proprietary format. Mol2mol is able to use this format.

Reaction files can also be inputted (only REACCS-type, CPSS format is not supported).

Atom types:

Elemental symbols are used. Lone pairs are not used in older MDL programs. Query atom types will not be preserved during the conversion.
Bond types:
1, 2, and 3.
The 4 (aromatic) and 5-8 (query types) are for data base use. However, on importing from another file format, aromatic bonds can be preserved. They will appear as dotted lines in ISIS programs, or represented by a circle in ChemWindow.
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MDL SD file   (read & write)
MDL RD file   (read)
*

The MDL's SD (structure data) file contains the structural information and associated data items for more compounds. In fact it is a multiple MDL file with added data items. You can select and input one structure only, or use the browse mode. The associated data items of the current structure appear in the text window.

You can write an SD file only if another multiple structure data file was opened in multiple mode. All of the structures of the input file will be passed to the output SD file. You can unify several simple files to an SD file by using the batch/merge I/O mode, or slice an SD file to several simple ones by the multiple/split mode.

RD (REACCS-type reaction data) files contain the structural information and associated data items for several reactions. In fact it is a multiple MDL reaction file with added data items. You can select and input one reaction only, or use the browse mode. The associated data items of the current structure appear in the text window.

Mol2Mol shows stereo bonds as well as heteroatom symbols and atom aliases, and adds implicit hydrogens in 2D files, if necessary, therefore you can easily browse sdf or rdf database files:

Reaction example


CSRR and Desktop Molecular Modeller (DTMM)   (read & write) *

The DTMM format has evolved from the originally crystallographic CSSR format, they were very similar. While CSSR format did not change, by now DTMM 4.0 differs considerably, therefore when writing this file format, it has been split to two subtypes. Selection is to be made in the Save file window.

The last item of the atom data lines of CSSR files is the atom group number. As far as I know no program has any use of it (although sometimes it is requested item). Mol2Mol writes the number of connections to here.

Bond types:

No bond types are used, files contain only connectivity information
CSSR: max 8 bonds.
DTMM: unlimited, but Mol2Mol reads the first 10 only.
Atom types:
Elemental symbols are used. However, DTMM molfiles may contain their own extended atom types as numbers. Mol2Mol only reads these. Dummy atom symbol: Xx (CSSR), -- (DTMM). Labelled atom names are supported (C11, N6 etc).

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PCModel   (read & write) *

The PCM file format produced by version 4.0 (or later) of PCModel can be read into Mol2Mol. Mol2Mol will only accept the basic structural information, i.e. only AT, B and C markers, not substructures, M, and other flags are taken into consideration. The same restrictions apply on writing PCM files from Mol2Mol. (To produce files that can be used by very old versions of PCModel, convert to Z-matrix files using the MOPAC suboption.) On loading the file into PCModel, use the MOPAC option to read the file. It is advisable to check the atom and bond types, and it may be necessary to rotate the structure by 180 degrees about the Z axis (depending upon the version of PCModel).

If the source file contains aromatic atoms or bonds, Mol2Mol asks how they are to be treated. Select single/double bonds for example, if you want to use pi-atoms and VESCF calculations in a planned MMX minimizations, but select the aromatic options, if the MMX force field calculation is intended to be used with simple averaged 1.41 Å aromatic bonds. Refer to the PCModel documentation for further details.

Bond types:

1,2,3 and 9 (complex bond)
Atom types:
1 sp3 carbon
2 sp2 carbon, alkene
3 sp3 carbon, carbonyl
etc...

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HyperChem   HIN (read & write) and HCS (read) *

The atom types used in HyperChem files depend on the current MM setting in the program; Mol2Mol accepts all of them. If the HIN file comprises more than one molecule, you can choose whether the whole structure is loaded or only a part of it.

Files converted to the HIN format by Mol2Mol contain the atom types corresponding to the MM+ force field.

Files of HyperChem format may contain residue and chain (molecule) information in the case of biopolymers. Mol2Mol will regard such a file to a "genuine" PDB-compatible one, if it contains at least one standard residue name. If so, a green letters PDB will lit in the upper status bar. In this case residue etc info will be passed to new PDB, Sybyl mol2, Insight and MacroModel files (and vice versa).

! HyperChem does not support the MODELs in PDB files (everything will be inputted in one).
! HyperChem does not support the HIN files with protein CA carbon atoms only. The best to use the PDB format in this case.
! In rare PDB files there may be connection(s) between different chains. HyperChem does not support this, therefore it makes the appropriate changes. Mol2Mol does not concatenate chains, therefore do not convert such PDB (or any other) files into HyperChem format.

HCS files are produced by the Conformation Search module of HyperChem. They store the energy minimized low-energy unique conformations of the starting structure. The first structural entry in the file is a full one in HIN format, the subsequent ones are compressed. You can input all structures or one-by-one only, in browse or multiple modes as well. The spatial orientations of the individual structures in the file are arbitrary, you can rotate and translate (superimpose) them according to a template molecule by the superimposing module of Mol2Mol.

Geometrical data of the named selections, if any, can be inspected by the Utilities | More geometry menu option.

Hyperchem files can be outputted as a javascript variable for the use as an inline structure in the Jmol browser applet. Select the as JMOL variable radio button from the Save file dialog window.

Bond types:

s - single, d - double, t - triple, a - aromatic (used also in COO- and NO2)
Atom types:

LP-lone pair
HHhydrogen exept on N or O
HOHOH alcohol
HXHCOOH carboxyl
etc...

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Moby   (read & write) *

Use the Cartesian file I/O MOBY format options in MOBY for transferring the files. MOBY versions prior to 1.6 do not use bond order information. If you get the "Unknown file type" error message with an earlier version of MOBY, check the file with a text editor. The first line should read:

98 MOBY
where the number is the number of atoms in the molecule, followed by the word MOBY. If it is missing, add it manually, then save the file and input it again.

When saving a MOBY file, there is an option now to use zero bond orders instead of the normal ones. This might be necessary when intending to make optimizations in MOBY.

Bond types:
1,2,3, and 4 (aromatic)
Atom types:
33Hhydrogen on C
36Hhydrogen on O
37Hhydrogen on S
etc...

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Biosym Insight car   (read & write) *

Mol2mol supports the Cartesian coordinate file (.car or .cor) format of Insight II. The program reads both the archive 2 and archive 3 subformats, but writes the newer archive 3 one. Helix, periodicity or 2D information are not supported and are skipped.

An Insight molfile may contain one or several separate molecules, structures. In the latter case the program prompts which molecule(s) should be inputted. On the other hand, one molecule may contain several substructures (for example amino acids in a peptide), in this case the program inputs the whole molecule as one, but remembers the substructure information, and uses it in the forthcoming transformation, if possible. Mol2Mol will regard such a file to a "genuine" PDB-compatible one, if it contains at least one standard residue name. If so, the green letters PDB will lit in the upper status bar.

A special feature of the Insight format that connectivity and bond order information are placed into a separate molecular data file, which has the same name as the coordinate file, but with the .mdf extension, for example my_file.car (or my_file.cor) and my_file.mdf. You need to input only the .car (or .cor) file, Mol2Mol will look for the corresponding .mdf file and use it. If the .mdf file with the same name cannot be found (or it is corrupted), Mol2Mol will generate automatically the connectivities. So if transferring Insight molfiles between computers, be sure that both files have been moved or copied.

When writing Insight files, force field atom types are assigned as unknown (?) types (re-assigning will take place in Insight, when choosing a new force field type).

Atom types:  Natural atom types, lone pair: L
Bond types:  1.0, 2.0, 3.0, 1.5 - aromatic

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MacroModel   (read & write) *
Maestro   (read & write)

Both molfile types may contain one or several separate molecules or structures. In the latter case the program prompts which molecule(s) should be input. On the other hand, one molecule may contain several substructures (for example amino acids in a peptide), in this case the program inputs the whole molecule as one, but remembers the substructure information, and uses it in the forthcoming transformation, if possible.

In the case of writing a Macromodel or Maestro file, upward transformation is necessary because of the extended atom types. If the calculation of atom types is not possible (lack of hydrogens), the general atom types will be used instead. It is possible to create user's atom types in Macromodel or Maestro, in this case you have to edit the molfile manually and change the appropriate atom types, or you can do it in those applications too.

The files may contain residue, chain and model information in the case of biopolymers. Mol2Mol will regard such a file to a "genuine" PDB-compatible one, if it contains at least one standard residue name. If so, the green letters PDB will lit in the upper status bar. In this case residue etc info will be passed to new PDB, HyperChem, Insight and Sybyl mol2 files (and vice versa).

In the case the Maestro files both the compressed and uncompressed formats are supported.

Atom types:

1   sp carbon
2   sp2 carbon
3   sp3 carbon
etc...
Bond types:  0 (transition states and coordination complexes),1,2,3, and 4 (bond of undefined order).

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Tinker   (read & write) *

Tinker dialog TINKER is a molecular modeling software package for molecular mechanics and dynamics, it has the ability to use several common parameter sets (http://dasher.wustl.edu/tinker). Because of this, in order to assign the atom types, each coordinate file (*.xyz) is accompanied by a key file (*.key). If no key file is present (or the force field type in it is unknown to Mol2mol), Mol2mol displays the dialog and prompts you to select the appropriate force field. If you select assign by atom names, the program tries to interpret these as elemental symbols (this is not a foolproof procedure).

Atom types:   force field atom types, or atom names/elemental symbols, lone pair (Lp), dummy atom
Bond types:  connectivities only.
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CACAO car   (read & write) *

The CACAO (Computer Aided Composition of Atomic Orbitals) program package may use internal or external coordinates, Mol2Mol supports the latter in CACAO 98 format, the use of crystallographic or Cartesian coordinates. As most quantum chemical programs, CACAO files do not contain bond information, these are generated during the input.

The output CACAO file will contain a header of general options, it can be edited manually if necessary. It contains Cartesian coordinates with crystal fractional parameters a,b,c, alpha,beta and gamma set to 1, 1, 1, 90, 90, 90, respectively.

For further details see: Mealli C. and Proserpio D.M.: CACAO, in MO Theory Made Visible. J. Chem. Ed., 67, 399 (1990); Internet: cacao.issecc.fi.cnr.it

Atom types:  elemental symbols

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ChemWindow (read & write) *

In ChemWindow, use the MOL file format for export/import of individual molecules, not the CW2 format.

Bond types:

1, 2, 3 and 4 (aromatic). Aromatic bonds in the case of rings will be represented by a circle.
Atom types:
Elemental symbols may be used.


Brookhaven Protein Data Bank   (read & write) *

* Mol2Mol only supports a subset of Brookhaven Protein Data Bank (PDB) record types. For the time being, the mmCIF format is not supported.
Mol2Mol supports four PDB subformats: the “classical” one, the 1996 revised format, the PDBQ format (containing atom partial charges, if available) and Chime/Rasmol format. The latter has been extended to support double and triple bond info and may also contain partial charges. In addition, the program automatically supports the PDB Fat (PDBF) subformat (used for example by VEGA), when the partial charges are added in the REMARK 77 EXTRA record. In addition, the program automatically supports the PDB Fat (PDBF) subformat (used for example by VEGA), when the partial charges are added in the REMARK 77 EXTRA record.

* On loading a PDB file into Mol2Mol, only the ATOM, HETATM, TER, MODEL and CONECT records are interpreted. In most cases this is sufficient to provide information on the three-dimensional structure of the molecule. Note that hydrogens are usually not included into PDB files, therefore prior to upward transformations add them with the Edit | Add hydrogens option.

The residue and chain information of peptides and nucleic acids will be passed to HyperChem, Insight, Sybyl and MacroModel files. Other programs may not treat and write into files these information. Alternate locations for one or more atoms will be inputted as they are. These can be removed via the Protein/DNA | Remove alternate locations option

In order to accept a file as a PDB file, Mol2Mol has to find three characteristic record type identifiers in the file (ATOM, HETATM, CONECT, END etc). Sometimes in very simple files only HETATM (or ATOM) and END can be found, and the recognition will fail. If this happens:

1) add a REMARK line to the beginning of the file manually using any ASCII text editor:

REMARK  any text
HETATM   1   C   1   -1.809   -0.151   0.164
HETATM   2   C   2   -1.666    1.173   0.281
. . .
END
2) or switch to manual mode. PDB files containing only the CA backbone carbon atoms are supported. As the resulting "molecule" is chemically nonsense, upward transformations and export to other modeling programs may led to strange results and/or error messages. However, no problems should arise when exporting into a drawing program.

The program supports the MODEL records, i.e. when multiple structures are presented in a file, as is often the case with structures determined by NMR. Similar files may contain the structures resulting from a molecular dynamics experiment. If such is the case and each model contains more than one chains, the structure selection dialog window may pop-up twice: first to select one or more models, and if only one of the models was selected, second times.

Mol2mol tries to figure out whether a PDB, MacroModel, Sybyl or Insight file contains proteins or DNA or RNA with standard residues. In the case of PDB files it is straightforward and the green letter PDB in upper status bar signals that the inputted file is regarded to a "genuine" PDB file. This means that subunit information (residues, chains, models) are available, the input file contained them.
indicator
If a Brookhaven PDB file contains HELIX, SHEET and/or TURN info, these will be inputted and the letters H, S or T signal at the upper status bar. The molecule can be coloured by these in the graphics window.

* On writing a PDB file from Mol2mol, only a subset of the PDB format is used (ATOM, HETATM, TER, MODEL and CONECT records). In the Save file dialog window you can select one of the above mentioned four subtypes.Contrary to high-end modeling programs with a built-in amino and nucleic acid residue library, Mol2mol cannot calculate atom types of biopolymers (peptides, nucleic acids) but can use if it is presence in the source file.

If the current structure is a "genuine" PDB one (as it is signalled by the green letter PDB in upper status bar), ATOM, HETATM records, residue and chain (and model) information will be passed into the new file. HyperChem, Sybyl, MacroModel and Insight source files may contain every necessary information. The atoms of standard residues (like ALA, GLY, LEU etc) are passed as ATOMs, the atoms of nonstandard groups as HETATMs.

If the input file is not regarded to a "genuine" PDB compatible one, all atoms are written to the HETATM records, and connectivity information to the CONECT records. On clicking the lit green PDB signal, it can be turned off - in rare cases you may want to use only HETATM records in the output file even if residue and chain information are available.

Use this output format only if it is necessary to load a structure into a program that only accepts PDB input, or for example if you want to cut one of the protein chains or substrate molecule from an assembly. Of the sample files installed into the /OTHERS folder, OXYTOCIN.HIN, PDB1FJA.ENT, 1CFC_CA.ENT, MACROMOD.OUT and 1SOX_BCHAIN.PDB are such files, which are good for experimentation.

If several files are unified into one by using the batch/merge mode, the output PDB file contains these as separate MODELS. By definition the MODELs in a PDB file are supposed to be structurally identical differing only in their conformations. Therefore when different molecules are merged, the resulting file, though technically correct, may give rise to problems in other programs.

By default, Mol2Mol writes the CONECT records of the MODELs into the MODEL the connection data belong to, respectively. Some programs expect that all of the CONECT records are placed at the end of the file. If the Preferences 2 | CONECT records to the end check box is set, Mol2Mol creates the new file in this manner.

By default, Mol2Mol numbers continuously the residues within one file (or MODEL), throughout all chains. If the Preferences 2 | Restart residue numbering in chains check box is set, residue numbering starts from 1 in every chains. In the PDB files both varieties can be found.

As PDB files produced by different programs can be quite diverse in format, different programs may interpret the same file in different ways.

more Protein utilities

Bond types:

Connectivity information is only used in special cases. ("non-standard" groups, HETATM records, H-bonds etc).
Atom types:
Special named atoms in ATOM records, natural atom symbols in HETATM records. A few programs put named atoms into HETATM records. These may be interpreted wrongly (for example CE3 as Ce). In this case manual editing is necessary.
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ChemDraft   (read & write) *

Only pure molecule files are used. Within ChemDraft III set the Cartesian mode in the File type... option prior to exporting or importing.

Bond types:

1, 2, 3 and up/down, dashed etc stereo bonds are supported.
Atom types:
Elemental symbols

Beilstein's ROSDAL   (read) *

Several programs use this type of format (CrossFire, Current Facts on CD ROM, Beilstein's Molkick, Excerp). They possess a very user-friendly and sophisticated two-dimensional molecule editor, so you may sometimes wish to import from this format. Simple Rosdal strings can be inputted as well. The .STR or .ROS files created may contain as many molecules (INOs) as you like. query options, Markush structures are not preserved by Mol2Mol, query atoms are translated to dummy atoms. However, up/down/either/ stereobonds can be imported to CPSS and ISIS programs, ChemWindow, PLT and ChemDraft. On loading, Mol2Mol prompts you for the INO (identification number within the file) of the required molecule.

The most simple way of moving a structure from CrossFire or Current Facts on CD ROM into Mol2Mol, if the hit molecule is transferred into the Structure Editor and then it is copied to the clipboard as Rosdal text. In Mol2Mol use the Open molfile | Clipboard option.

In the latest Crossfire versions and in files written by MDL programs the original file format has been changed somewhat, Mol2Mol 5.0 (or later) can input these as well.

When opening with a text editor, a typical Beilstein file looks like this:

Q1,00000000,STR ,000
CRC=00
INO=1
HSF=
OSF=
()1*(X4294,Y4991),2N(+1,X5447,Y5010),3N(X6739,Y5010),4*(X3261,Y4217),5*(
X3619,Y5784),1-5,1-4,1-2#3.
@@
and a simple Rosdal string:
()1(X1164,Y447),2(X1552,Y671),3O(X776,Y672),4(X1164),5N(X1941,Y447),6S(X
1551,Y1121),7(X388,Y448),8(X388),9(X2329,Y671),10Br(Y672),11N(X2718,Y443
),12(X2332,Y1122),13(X3111,Y665),14(X2725,Y1345),15(X3114,Y1117),16(X350
0,Y441),17(X2727,Y1797),1=4-8=7-10,1-3-7,1-2=6,2-5-9=12-14-17,9-11=13-16
,13-15=14.

If the program does not recognize a simple Rosdal string, try to use the manual mode set to Rosdal.

As these files contain only two-dimensional screen coordinates, all geometry calculations give nonsense results.

Bond types:

- for single, = for double, and # for triple
Atom types:
Natural atom types.
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MOPLO   (read & write) *

MOPLO prior to version 2.0 accepts only connectivities, therefore the different bond types are not preserved. Mol2mol reads both versions, but writes version 2.0 MOPLO files.

Bond types:

ver 1.x: Connectivities only
ver 2.0: 0 - single, 1 - aromatic, 2- double, 3- triple
Atom types:
elemental symbols and dummy atom (X).

CAChe   (read & write) *

The high-end modelling program Cache uses an intricate file structure with a large amount of different information. Only direct structural information are supported by Mol2mol. After importing a molecule into Cache, you may want to adjust the appearance of the atoms and bonds.

Bond types:  single, double, triple, complex, ionic, weak
Atom types:  elemental symbols and hybridization/valence state:

slinear
splinear
sp3tetrahedral
sd3tetrahedral
d2sp3octahedral
dzsp3trigonal pyramidal
dxysp3square pyramidal
p3trigonal pyramidal
dsp3square planel
unconfany
Lone pairs are allowed.

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Z-matrix   (read & write as user's general file or MOPAC or Gaussian) *

Z-matrices (sometimes called "internal coordinates") do not use Cartesian x, y and z coordinates, but atom-atom distances (r), angles (phi) and dihedral angles (theta) instead. They are used mainly by quantum chemical programs.

 Z-matrix read   write

As there are a number of variations of Z-matrices, the program offers four different possibilities for the inputting of Z-matrices. Sorry, but because of the many subtypes a fully automatic and reliable identification of them is nearly impossible, therefore you must know the exact format in order to select the appropriate one (it is not difficult).

A) The most general formats of Z-matrices
B) Gaussian type ZG-matrix
C) Gaussian Z-matrix with symbolics
D) Simple stand-alone MOPAC input file


     A) - This is the most general option

The Open general input option is intended to capture Z-matrices from the output files of different quantum chemical programs like MOPAC, Gaussian etc. These are usually long ASCII files containing Z-matrices and other data (see the sample file MOPAC.OUT). Before inputting, you must edit the file using any text editor. Look for the beginning of data in the file and, immediately before the coordinates, insert a new line starting with &&& (or GGG or $$$ in the case of a gaussian Z-matrix of type C). You can add a short comment after this marker, it will be interpreted as the name of the molecule. The data lines may be numbered, and the atomic symbols may be replaced by atom numbers (i.e. 6 for C, 7 for N etc).
Important feature of this type that the numbers of the defining atoms of bond lengths, angles and dihedral angles are placed after the geometrical data, at the end of lines (blue numbers). The table must end with a blank line. E.g.:

&&& Z matrix input example
    1   C
    2   H    1.0881                         1
    3   C    1.5801    28.0155              1   2
    4   C    1.5211    85.9867    0.0033    3   1  2
    5   H    1.0801   137.1030 -177.566     3   1  2
    .
    .
    n   H    .0404     114.1002  0.0033     11  8  9
    <empty line>
    ...other data...
or:
&&& Another possible format
    C 0.0000 0   0.0000 0   0.0000 0 0 0 0  0.123
    H 1.0881 1   0.0000 0   0.0000 0 1 0 0 -0.012
    C 1.5801 1  28.0155 1   0.0000 0 1 2 0   .234
    C 1.5211 1   5.9867 1   0.0033 1 3 1 2   .3045
    H 1.0801 1 137.1030 1 177.5660 1 3 1 2  0.023
    .
    .
    H 1.0404 1 114.1002 1   0.0033 1 11 8 9 0.011
    <empty line>
    ...other data...

You may notice in the second example, that supplemental data appears at the end of lines (red numbers). Some programs, e.g. BioSym Insight add atomic charges this way. Therefore the input routine asks for the presence of additional charge data. If it is present, the program inputs these as atomic charges.

If atomic charges are separately included in the input file, the charges can be also read in by using the @@@n marker immidiately before the beginning of the atomic charges. Substitute "n" by the column number of the charge data. For example:

    ATOM NO.   TYPE  CHARGE   ATOM ELECTRON DENSITY
@@@3
       1        C   -.047077     4.0471
       2        C   -.014849     4.0148
       3        C   -.167385     4.1674

After the data there must be one empty line. Only one @@@ marker may be in a file, and the charge data will be associated with the selected molecule (if more than one &&& or ### markers are used within the same file). Therefore care must be taken that the number of data (=atoms) should be the same in each case.

After each of the geometrical data, there may be marker symbols, such as "*" or "1" or "0" (shown in cyan in the above example), they are used for example in MOPAC or AMPAC internal files as a guidance for geometrical optimization. The program prompts for this; answer yes, if there are any (in this case every data item [r, phi and theta] must be followed be a marker character or string). More examples can be found in the sample files GENERAL.RES and MOPAC.OUT.

     B) ZG-matrix

This type of Z-matrix can found for example in the Gaussian output files (see the sample file G98.OUT), and we shall refer to it as ZG-matrix. Contrary to the other type of Gaussian Z-matrix, it contains no symbolic variables, i.e. the geometrical data are included as numbers. Contrary to to the above discussed type A, here the defining atoms (blue numbers) are placed between the geometric data:

$$$ ZG-matrix
   1   1  N 
   2   2  C     1   1.430000(  1)
   3   3  C     2   1.340000(  2)   1  122.000( 14)
   4   4  H     2   1.080000(  3)   1  118.000( 15)   3  180.000( 26)   0
   5   5  C     1   1.440000(  4)   2  115.000( 16)   4   23.000( 27)   0
   6   6  C     1   1.440000(  5)   2  115.000( 17)   3  -18.000( 28)   0
   7   7  H     5   1.343700(  6)   1  109.000( 18)   6  200.000( 29)  -1
....

There are also other differences, for example the numbers of the last column (green numbers 0, 1 or -1) are flags to help the interpretation of the Z-matrix. Use in this case the $$$ marker. Apart from the data in parenthesis, the structure of the matrix must look as in the example, contrary to the type A, no variations are allowed.

     C) Gaussian Z-matrix with symbolics

     D) Simple stand-alone MOPAC files

For convenience, there is a separate input option available for MOPAC input files. The direct input of this MOPAC format of Z matrices is available only through the manual input mode (Open file menu). The file format must be as defined in the documentation of MOPAC 6. However, in the case of problems you may want to edit the file manually and add the &&& markers as written above, and then use Open general... option for the input. If the input problem arises from an unusual header, edit the MOPAC file in the text editor (Edit | Edit last molfile, or any other ASCII text editor): there must be three lines of text at the beginning of the file. The first and third lines may contain any text, as they will be discarded. The first 20 characters of the second line will be accepted as the name of the molecule. In the fourth line the actual Z matrix data begin. A typical MOPAC input file begins like this (see the sample file MOPAC.INP):

EF GNORM=0.100 MMOK GEO-OK AM1 MULLIK PULAY
.
.
  C    0.000000  0    0.000000  0    0.000000  0    0   0   0
  C    1.408173  1    0.000000  0    0.000000  0    1   0   0
  C    1.389786  1  119.080032  1    0.000000  0    2   1   0
  C    1.397278  1  120.531311  1    0.000000  1    3   2   1
  C    1.392502  1  119.943802  1    0.000000  1    4   3   2
Use this manual MOPAC input option only for pure MOPAC input files and not for the output files of the calculations!

 Z-matrix write   read

These procedures assume you are familiar with Z-matrices to some extent and with the modelling program(s) you use.

Mol2Mol does provide some options for customizing the format in the form of a dialog box. You may add line numbers, character flags after the coordinates, choosing between the use of atomic symbols and atom numbers, choose the symbol for dummy atoms, add atomic charges as the last column, and specify the number of characters to the right of the decimal place. There is a separate MOPAC option using the most frequent parameters; this option will add three lines to the beginning of the file too. In the case of the AMPAC option a terminator line filled with zeros will be added. Gaussian option adds five lines to the beginning. All of these options can be set in a separate window:

Z-matrix

On writing a Z-matrix file, Mol2Mol prompts you for the first three atoms, these must be connected as a-b-c. The first atom of the Z-matrix must not be a hydrogen. The output should be regarded as containing only the most basic information. Different programs require different forms of input in the first lines.(e.g. flags for bond/twist angles etc.).

Three different methods are available for the Z-matrix generation. In the case of the "chain" method (default) the algorithm tries first to step along the longest chains of the molecule, and after them deals with the other atoms:

      11    13-14   17-18
      |     |       |
   10-9-8-7-6-5-4-3-2-1
        |       | |
        12     15 16
In the case of the "star" method the program tries to include every atoms connected to the previous one before advancing:
      16       11-12    3-4
      |        |        |
   17-15-14-13-10-8-6-5-2-1
	     |    | |
	    18    9 7
These are tendencies only and in fact, the numbering of the new Z-matrix depends strongly on the chosen starting atoms. Switch between the methods by selecting or resetting the Use star method check box in the Z-matrix parameter window.

You can select the manual method as well. In this case you have to click on all of the atoms in the graphics window in the desired order.

l In the screen output of the Z-matrix the original numbering of the atoms are added at the end of the lines. Using this aid you may check easily the stepwise construction of the Z-matrix.

Conversion to Gaussian and Gamess symbolic Z-matrix file:

Choose the Z-matrix option from the Convert menu, and then Gaussian or Gamess from the opening window. Some properties of the new Z-matrix can be optionally changed here. As different programs may use different headers, you may want to input and edit the header of the new file by the Edit | Edit last output file option.If you select the Gamess option, you have add the symmetry info as well. The molfile contains the full molecule, as if it would possess no symmetry (C1). In the case of Q-Chem the correction of the net charge and the spin multiplicity may prove necessary. Consult the appropriate manuals for the details.

beginning of Z-matrix
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X-ray CIF   (read and write) and CIF/MIF   (read) *

* Read:

This standard Crystallographic Information File (CIF) is a general archive file format, and it has been adopted by the International Union of Crystallography. Only the data codes determining the structure are taken into consideration.

Note that if the file does not contain hydrogen atoms, an automatic upward conversion is not possible (you may change this setting in the case of inorganic molecules in the Preferences).

For more details on the file structure see: Hall, S. R. et al.: Acta Cryst. A47, 655-685 (1991)

For the time being the mmCIF format is not supported. The CIF/MIF format is an extension of the CIF one: it may contain multiple structures as well as bond type information (1,2,3 and aromatic).

* Write:

This is a rarely useful option, as special crystallographic programs are better in creating CIF files, however, sometimes it can be useful in expert hands.

fract. filesSelect the Convert | X-ray option from the main menu, and CIF from the next option window. As a CIF file usually contains a great number of other data and several of them are essential for a crystallographic program, a perfect file will only be produced if the input file was also a CIF type one. In this case every data from the input file find before the coordinates (_atom_site_ data) and anisotropy data (_atom_site_aniso_ data) will be copied into the output file. If you previously made some editing in Mol2Mol (for example deleting an atom), the changes will be reflected in the appropriate fields (_chemical_formula_sum etc).

If the input file was a SHELX file, the CIF will contain some crystallographic data beyond the coordinates (Unm data will be passed too). In other cases the result will be a very rough one, but sometimes can be useful, for example if you have to create an input file for a drawing or plotting or modeling program, and it needs the CIF input format.

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CSD MODEL and FDAT files   (read) *

Two file formats of the Cambridge Structural Database are supported, the MODEL (*.MDL) and the FDAT (*.DAT) files. Both formats may contain multiple entries. The MODEL files are supposed to include connectivity and bond-type information, and have Cartesian coordinates. Single, double, triple and aromatic bond types are retained, others (pi, conjugated) will be marked as aromatic bonds. To re-assign them to single/double bonds, make an upward transformation to, say, Alchemy, then, if necessary, to another appropriate downwards format. Note that the MODEL format is in an experimental phase and may change in the future.

l Note also that if the file does not contain hydrogen atoms, an automatic upward conversion is not possible (you may change this setting in the case of inorganic molecules in the Preferences, or add hydrogen atoms prior to the conversion). If in the case of coordinative compounds there are bonds between the metal atom(s) and the ligand, remove these prior to the adding of the hydrogens or change them as coordinative bonds from the graphics window.

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General free format X-ray file   (read) *

* Read:

Crystal coordinate files may begin with any number of comment lines, each of which must begin with the character > or #. The first comment line is regarded as the name of the molecule, and is truncated to 30 characters on being read into Mol2Mol. The first data line must contain a number representing, in sequence, a, b, c, alpha, beta, and gamma. The following lines contain the atomic symbol and the atomic coordinates, which may come before or after the symbol. These lines may optionally begin with a line number, e.g.:

     >5-methoxy-menninkeinin; component of klingon udd-hu
     >Tetr. Lett. vol 524., 9999 (2499)
     >Picard, J.-L., Riker, W., Troy, D. et al.
     2.345  4.556  5.555  90.000  110.55  90.000
     1  C      0.6789   1.2222  1.2349
     2  C      1.0001   1.3452  2.4444
     3  ...etc.
     .  ...
     n  ...
or:
     ...
     0.6789    1.2222   1.2349  C
     1.0001    1.3452   2.4444  C
     ... etc.

The use of labelled elemental symbols is allowed: C(1), C2B, Cl(3), S6 etc. The second character, if a letter, will be regarded as part of the atom symbol. Therefore symbols like HA or HB are not allowed.

* Write:

Select the Convert | X-ray option from the main menu, and General from the next option window. In a third option window you may decide how to add the atom symbols to the coordinates. The output will look for example:
Name: c48rc 
Created by Mol2Mol 3.50  Wed 26 Apr 2000 22:12:11
from C48RC.CIF of type CIF

   15.361   15.361   17.334   90.000   90.000   90.000
O          0.510    1.403   -0.317
H          0.534    1.428   -0.279
C          0.422    1.336   -0.154
C          0.450    1.323   -0.218
... etc
You may manually edit the file according to your needs.
fract. files

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General free format Cartesian file   (read & write) *
* Read:   write

This option is intended to capture Cartesian coordinates from the output files of different quantum chemical programs like MOPAC, AM1 etc. Before inputting, edit the file using any text editor. Look for the beginning of the data in the file and, immediately before the coordinates, insert a new line starting with ###. You can add a short comment after this marker that will be interpreted as the name of the molecule. You may place more markers in a file. The data lines may be numbered, and the atomic symbols may be replaced by atom numbers (i.e. 6 for C, 7 for N etc). The table must end with a blank line. E.g.:

           ###molecule 1
           C  1.2222    2.3333    0.3333
           .
           .
           H  4.6060    0.3456    0.0101
           <empty line>
           ...other data...
or:
          ###molecule 1
           1    6    1.2222   2.3333   0.3333
           .
           .
           n    1    4.6060   0.3456   0.1010
           <empty line>
           ...other data...             

The spacing of the columns is not critical (free format). The sample file GENERAL.RES contains examples of the combinations of formats supported.

The use of labelled atom symbols is allowed: C(1), C2B, Cl(3), S6 etc. The second character, if a letter, will be regarded as part of the atom symbol. Therefore symbols like HA or HB are not allowed.

As the program has to distinguish between integer and decimal numbers when parsing the format, the use of 0 instead of 0.000 in the first line may lead to false interpretation.

MOPAC-type flag characters after the coordinates are allowed (similarly to Z-matrices) between the Cartesian coordinates:

### 
C    0.10134  1  1.40055  1  -0.34560  1
C    2.80302  1  1.50000  1  1.23867   1
C    2.10703  1  1.23867  1  0.00000   1
...

If atomic charges are separately included in the input file, the charges can be also read in by using the @@@n marker immediately before the beginning of the atomic charges. Substitute "n" by the column number of the charge data. For example:

    ATOM NO.   TYPE  CHARGE   ATOM ELECTRON DENSITY
@@@3
       1        C   -.047077     4.0471
       2        C   -.014849     4.0148
       3        C   -.167385     4.1674

After the data there must be one empty line. Only one @@@ marker can be in a file, and the charge data will be associated with the selected molecule (if more than one &&& or ### markers are used within the same file). So care must be taken that the number of atoms should be the same.

Cartesian variations

 

On the whole, the following
variations are allowed:

The spacing of the columns is not critical (free format). The sample file GENERAL.RES contains examples of the combinations of formats supported. As the program has to distinguish between integer and decimal numbers when parsing the format, the use of 0 instead of 0.000 in the first line may lead to false interpretation.

* Write:   read

This option writes only the Cartesian x, y, and z coordinates into the file, no bond or other information are added. This is useful, if you need only the geometrical information in another application. You may choose whether 3D coordinates, 2D coordinates with zeroed z values, or only x and y coordinates are printed into the file, as well as atom numbers or symbols are to be included.

x, y, and z coordinates:
    0.07373 0.26824 1.02020
x, y coordinates and 0 for the z coordinates:
    0.07373 0.26824 0.00000
x, y coordinates only:
    0.07373 0.26824
atom symbol before x, y and z coordinates:
    C 0.07373 0.26824 1.02020
atom number before the coordinates:
    6 0.07373 0.26824 1.02020
atom symbol after the coordinates:
    0.07373 0.26824 1.02020 C
atom number after the coordinates:
    0.07373 0.26824 1.02020 6
Gamess style:
    header
    C 6.0 0.07373 0.26824 1.02020
Q-Chem style:
    header
    C 0.07373 0.26824 1.02020
Write Cartesian coordinates options dialog

Optionally you may add numbering to the atom (elemental) symbols in two different ways:

Unique number for every atom: C1, C2, C3, H4, H5, O6 etc
Unique number for each element: C1, C2, C3, H1, H2, O1 etc.
”Lettered” hydrogens: the numbers of hydrogens are derived from their parent atom, and are distinguished by the letters A, B, C, if they have a common parent atom (CH3 etc groups → H4A, H4B, H4C).


Optionally you may add line numbering to the beginning of lines, and output the coordinates in angstrom or nanometer units.

In the case of Gamess and Q-Chem formats some header and footer lines are also added. You probably may want to edit these lines according to the input parameters of the calculation.You have add the symmetry, multiplicity info etc as well. The molfile contains the full molecule, as if it would possess no symmetry (C1). Consult the appropriate manuals for the details.

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Gaussian Z-matrix   (read & write) *

This special subtype of Z-matrices' is used by the ab initio quantum mechanical program Gaussian.

The input of Gaussian Z-matrices is possible:

a) From a user's general file by capturing the matrix, similarly to Cartesian coordinates or normal Z-matrices. In the case of a Gaussian Z-matrix place the marker GGG immediately before the beginning of the coordinates, as in the example below.
l In the case of Q-Chem it is not necessary (but may, in the case of problems), as that program uses an appropriate token ($molecule) useful for recognizing the coordinate section.

b) Stand alone Gaussian Z-matrix input files can be inputted via the manual mode too, switched to Gaussian. In this case no GGG marker is necessary, but file must have a standard header: by default there must be exactly 5 lines before the beginning of the matrix data (some of them can be empty lines). However, if more than one # or % lines appear, they are taken into account. Any text appearing in these lines will appear in the text window as remarks. Don't use this manual mode for files originating from Q-Chem, Gamess or other programs.

%chk=g12r_g94_1903.chk

my_molecule

0 1 
name_of_the_molecule_can_be_here
    8					 0.1234
    6    1 R2				 -0.0123
    6    2 R3     1  A3			 -0.025
    6    3 R4     2  A4     1  -T4    0	- 0.025	    
    6    1 R5     2  A5     3  T5     0	 -0.11
    1    2 R6     1  A6     3  T6     0	 -0.11
    6    2 R7     1  A7     3  T7     0	 -0.11
    1    3 R8     2  A8     1  T8     1	 -0.005
    1    3 R9     2  A9     1  T9    -1	 -0.005
    1   31 R34    28 A34    25 T34    0	 0.005
    1   31 R35    28 A35    25 T35    0	 0.011
    1   31 R36    28 A36    25 T36    0	 0.011

R2 =    1.44020
R5 =    1.36993
R7 =    1.52956
T12 =   177.7497
T19 =   179.6816

R3 =    1.54891
R4 =    1.52664
R6 =    1.11423
R8 =    1.10625
R9 =    1.10364
R10 =    1.10502
R11 =    1.10547

As you may see in the above example, the first part of the Gaussian Z-matrix is similar to the normal Z-matrices. The order of presentation is different. An atom (real or dummy) is specified in the format:

Element N1 Length N2 Alpha N3 Beta jflag charges

Element can be chemical symbol (C, H, O), number (6, 1, 8) or named atom (C1, N2, X3). Length, Alpha, and Beta are the bond lengths, the angle, and dihedral, respectively. They can be real, e.g. 1.45, 109.4, 180.0, or symbolic. A symbolic is an alphanumeric string of up to 8 characters, e.g. T5, A2. The Z-matrix itself is terminated by a blank line, after which come the values of the symbolics, one per line. There may be a blank line in this set (the set before the blank line is optimized, all symbolics after the blank line are considered fixed in the modelling programs). The input process stops at the second blank line (or if the end of file is reached) The symbolics and its value my be separated by a space, comma or equal sign.

Further optional columns may be present or not. The very last column may contain atomic charges (red numbers), Mol2Mol prompts you during the input as it needs this information. The green numbers (jflags), if any, supply further information on how to interpret the Z-matrix. Their presence or absence is detected by the program automatically.

Conversion to Gaussian, Gamess and Q-Chem Z-matrix file:

Choose the Z-matrix option from the Convert menu, and then Gaussian from the opening window. Some properties of the new Z-matrix can be optionally changed here. As different programs may use different headers, you may want to input and edit the header of the new file by the Edit | Edit last output file option. If you select the Gamess option, you have add the symmetry info as well. The molfile contains the full molecule, as if it would possess no symmetry (C1). In the case of Q-Chem the correction of the net charge and the spin multiplicity may prove necessary. Consult the appropriate manuals for the details.

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Xmol   (read & write) *

This file format of the (originally) Unix program Xmol contains only simple atom types and no bond information is included. The input file can be a multiple one, in this case Mol2Mol prompts for choosing one structure. As this is a very simple format and its recognition may sometimes interfere with other file types, in the case of problems switch to the manual input mode. The second line of the file (or the corresponding ones in the multiple structure files) contain textual information. The first 40 character is regarded as the name of the molecule.

From Mol2mol 5.4 the old Unichem xyz subformat is supported again (can be useful in certain situations).

Xmol-type xyz files can be outputted as a javascript variable for the use as an inline structure in the Jmol browser applet. Select the as JMOL variable radio button from the Save file dialog window.

Atom types: Elemental symbols


Mxyz   (read & write) *

This file format is similar to the Xmol format but bond information is included. The input file can be a multiple one, in this case Mol2Mol prompts for choosing one structure. As this is a very simple format and its recognition may sometimes interfere with other file types, in the case of problems switch to manual input. Note that the numbering of the atoms in the connectivity table starts with 0.

Atom types: Elemental symbols
Bond types: 1-2-3

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PLUTO   (write) *

PLUTO is a widely-used plotting program, which generates HPGL (Hewlett-Packard Graphics Language) files. Mol2Mol creates an input file for PLUTO containing only the most basic information. As there have been several different PC and work station versions of PLUTO, you may need to customize the PLUTO input file produced by Mol2Mol to suit your version, refer to the manual of your PLUTO version. However, Mol2Mol allows you to set some fundamental parameters in the plot file parameters dialog box (title, resolution and atom labels). Different programs may omit several of these. The file generated by Mol2mol contains Cartesian coordinates. In this case the CELL parameters at the beginning are written as:

	CELL 1.00 1.00 1.00 90 90 90
Some programs require:
	CELL 100 100 100 90 90 90
In some cases this line can be omitted at all.
Plot file parameters dialog window
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WinPLT   (write) *

WinPLT 7.1 (DOS PLT ver 5.1 or later) is a program for drawing, plotting and printing high-quality chemical structures to a variety of printers and HPGL plotters (DOS version) or WMF/EMF format (Windows version). Mol2Mol can only write the most basic structural information to PLT files. Double, triple, wedged, hatched etc bonds are retained, if possible, and hetero atoms are added as labels. However, when the file is read into PLT, you will have to clear the hetero atoms from the overlapping bonds in the J-EDIT label routine (DOS version) or by pressing ctrl-space_bar (Windows), flip the double bonds if necessary, and resize the structure. Mol2Mol also tries to figure out whether a left, right or middle double bond is necessary in a given place, however, you may need to check and correct the structure. Mol2Mol allows you to set the hydrogen parameters in the plot file parameters dialog box.

The fourth option, implicit heteroatom hydrogens is interpreted in two different ways:

a) If the molecule contains explicit hydrogen atoms, all C-hydrogens will be removed, N,O,S,P-hydrogens will be converted to implicit hydrogens, all other hydrogens will retained. Bond types are not used for this type of coversion.

b) If no hydrogens are present in the molecule, implicit hydrogens will be added to non-metals and to the Ia and IIa-column elements, but not to transitional metals. The same rules are applied, as in ISIS/Draw in “hydrogen labels on hetero atoms” mode. Standard valences and formal charges (if present) are taken into consideration. Bond type info (1-2-3 etc) is necessery!

Atom types:  Every symbols are accepted
Bond types:  1,2,3 and several stereo bonds

Plot file parameters dialog window


WIMP   (write) *

WIMP 2001 files contain multiple bonds in vectorized form, Mol2Mol cannot do this, so all bonds will be single bonds. Changing back to multiple bonds must therefore be done within WIMP once you have loaded a structural file created by Mol2Mol. Heteroatoms are added as labels. When loading the file into WIMP, use the FTR file option. You may need to resize the structure.

Mol2Mol allows you to set the hydrogen parameters in the plot file dialog box. If you select the "No hydrogens" option, Mol2Mol removes the hydrogen atoms from the molfile, therefore input the file again if you need it.

Plot file parameters dialog window
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SCHAKAL   (write) *

Input files can be generated for this high-level plotting program. To load the file into SCHAKAL use the I U command and then type the input filename, without its extension. Mol2Mol uses the .dat extension as the default for SCHAKAL files. Your SCHAKAL program should also use this default extension, check for this if you experience problems. You cannot specify any plotting parameters within Mol2Mol. These can only be set from within SCHAKAL.


POV-Ray   (write) *

POV-Ray dialog

The ray tracer program POV-Ray 3.1 is for creating very high quality three dimensional, photo-realistic 24-bit images. By editing a POV-Ray input file and using its scene description language you can endlessly vary the colours, textures and lightning of the scene, and create professional images for www pages. Mol2Mol will generate a standard input file from the molecular coordinates in order to create images according to your wish. Camera and light positions are also calculated.

Model, bond and colour options:

* Model: Spacefill (CPK) as spheres or blobs, vector or ball-and-stick models can be selected. *

* Cylinders: In the case of vector models the thickness of vectors can be set.
   This first two options can be separately set for the whole image and a selected part of it.
*

* Bonds: Available when ball-and-stick models are used; the coordinate, weak, dummy and other special bonds are always drawn as dashed cylinders. *

* Bond color: The bonds can be coloured with the default colour, or with the corresponding atom colours. In the latter case simple or gradient fill colouring can be applied. For splines or delocalized rings the latter is not used. *

* Selection color: If a molecule or part of it is selected in the graphics window, this will influence its appearing in the POV-Ray image. It will be colored as it appears in the graphics window, or according to the atoms, or according to the partial atom charges (left image). Similarly, if the current structure is coloured according to the models, chains or residues, the image will be coloured accordingly. The defined colours can be found and changed at the end of the POVCOLOR.DAT file. *
Other atom properties inputted separately can also be mapped. Right image: an active center with its substrate.

Colouring by charges *

Miscellaneous options:

* Shadow on/off: The casting of shadows can be switched on or off. However, this option has no effect if the light_source object is defined in the actual pod file.

* Toggle hydrogens: The displaying of hydrogens can be switched on or off in the Graphics window. If the Toggle hydrogens of the selection option is set, the displayed state of the hydrogens of the selected part of the molecule is the opposite to the H-button of the Graphics window.

* Atom labels: Atom, bond, resiue etc. numbering can be added to the end of lines as remarks, these are useful if you want to edit the file manually later.

* Spline backbone: If only the backbone atoms of a peptide are displayed (Utilities menu|Peptide backbone), or the molfile contains only the CA atoms, the backbone will be represented as a smooth tubular spline, when activating the Spline backbone option. As the spline is approximated with a large number of small cylinders and spheres, the resulting POV-Ray file can be very large! Disulphide bonds will be shown as separate atoms. This option cannot be used with cyclopeptides. The splines are always coloured according to the screen and the chain must have at least three residues. Spline

Spline suboptions:

Splines
* Perspectivity: This option adds a slight perspectivity effect to the image: the size of the atoms and the tapering of the bonds will be varied by the depth. The use of this option may slow down the rendering of the image in POV-Ray. Does not work with spacefill models. Perspectivity

* Colour perspectivity: This is another option to emphasize the three-dimensionality: the colour/brightness of the structure will be varied according to the depth. The amount of the effect can be changed in the POVCOLOR.DAT file (col_persp). Colour perspectivity

* Black and white images: Black and white images can be created with/without (hetero)atom labels and/or crosshatches. Black and white images should always be rendered in antialiased high resolution mode. If small images are necessary, such as this example, resize a high resolution image with Photoshop or another appropriate application. Black and white images

* Coordinates into separate file...: Option for writing the coordinates into a separate include file. This greatly helps the manual editing and customisation of the pov files, especially in the case of big molecules. The name of this include file is the same as that of the pov file but with the .inc extension and is written into the same folder, such as bigbang.pov and bigbang.inc. Move or copy the files together into a new folder!

* Autofit according to…: Normally the image will be sized that all of the atoms will fit into it. If part of a biopolymer is selected and the Show only selected... option is active, the visible part will be enlarged, when the Autofit according the visible atoms only check box is set.
If you want to fine tune the size of the molecule in the POV-Ray image, edit the next line in the beginning of the created *.pov file in the POV-Ray editor:

   camera {location <  0.543,  -0.851, -319.127>
As the molecule is usually located around 0 on the z-axis, by raising the z-position of the camera (red number), the image will be magnifyed.

Rings:

* Shade rings: The planar or all of the 3-7 membered rings will be transparently filled when selecting one of the Shaded rings options. The shading colour is defined by the entry “Color_ring_fil” in the POVCOLOR.DAT file. Shaded rings

* Aromatic bonds as circles: 5-7-Membered aromatic planar rings will be drawn with circles (tori), if the Aromatic circles option is selected. The colour of the circle (torus) is defined by the entry “Color_arom_circle” in the POVCOLOR.DAT file Aromatic bonds as circles
Buttons:

Edit *.pod file: Opens the file editor and loads the selected *.pod header file (see below).
Edit povcolor.dat: Opens the file editor and loads the POVCOLOR.DAT file (see below).
Create colours: Opens the Windows colour dialog window. You may choose or create a new colour. After closing the window the red, green and blue components of the selected colour will appear in the text window. These values can be used for modifying a *.pod file or a previously created *.pov POV-Ray input file.
Override colours: Opens the element colour window. On double-clicking on an element colour, this selected colour will override the atom colour defined in the POVCOLOR.DAT file. If you happen to create images from SHELX files and it contains Q atoms, the colour of lawrencium (the last element) will always be applied.

More about colours, pov and pod files

* A special option for advanced users is the use of header & footer files (*.pod). The content of these text files is merged automatically to the beginning and the end of the generated POV-Ray input file. The headers and footers may contain any text written in POV-Ray's language, defining additional objects, textures, colors, etc. So if you are an advanced POV-Ray user, you can write different *.pod files (these must be placed into the parent Mol2Mol program directory), and later you can simply choose any of them and generate quickly the desired POV-Ray input file (*.pov). The structure of the *.pod files can be understand from the following example:

Sky blue background with wood ground        // max two lines before *header*
*header*
#version 3.0
global_settings {assumed_gamma 1.0}
#include "colors.inc"
#include "textures.inc"
#include "stones.inc"

light_source { <-15,20,0> Red * 3      //!! if used, Mol2Mol will not calculate
    spotlight                          //    and add its own light_source object
    radius  1
    falloff 4
    point_at -y
}

*footer*

camera {angle 22}         //!! Mol2Mol calculates the basic camera positions, but
                          //   you may modify them here
plane {
    <0,1,0>, %ymin%       //!!  %ymin% : Mol2mol variable, see later
    texture {
            T_Stone23 scale 3
            }
       }

fog {
   turbulence <.4, .2, .2>
   color SkyBlue
   distance 400
    }

At the beginning there may be max. two lines of information, this will appear in the menu window. Everything between the markers *header* and *footer* will be added to the POV-Ray file before the description of the molecule. Everything after the marker *footer* will be added after the coordinates of the molecule.

Six special Mol2mol variables can be used in the *.pod files. They will be replaced by their actual numerical values during the generation of the POV-Ray file. The variables %xmax%, %xmin%, %ymax%, %ymin%, %zmax% and %zmin% designate the modified highest and lowest values of the x,y and z coordinates of the molecule. For example %ymin% is calculated as:

%ymin% = ymin - RVdW -1

where ymin is the y coordinate of the "lowest" atom, and RVdW is van der Waals radius of this atom. These are very useful, if for example you want to place a plane under the molecule, as in the above example. The next scheme shows the definition of %xmin%, %ymin% and %zmin%:

*

10 different sample *.pod files are installed into the program folder, for example the file sample9.pod produces the following type of image:

sample9.jpg

 * Colour of atoms and the bonds in the POVCOLOR.DAT file:

Mol2Mol uses 106 colours for colouring the different atoms (103 elements + lone pair + dummy atom + deuterium), 32 for residues, chains and models, and a few others for specific purposes. These are defined in the file POVCOLOR.DAT. You may edit this file in order to change the default colours, as written in the header of that file. You may use the colours already defined in POV-Ray: Bronze, Orange, Sienna and alike (consult the documentation of POV-Ray), or your own colours can be specified by the expression:

rgb <1.0, 0.75, 0.65> or color <1.0, 0.75, 0.65>

where the three values (red, green and blue components) should be in the range of 0.0 to 1.0. For convenience, use the Edit color button to create a new colour.

Alternatively, you can use the atom colours defined in the element colour window (Override color)

 * The finishing of the surfaces can be influenced by changing the parameter of the Finish entry. The default is "Shiny", but you may use any predefined in the POV-Ray: "ambient", "Dull", "Phong .5" etc. Full expressions can also written, but only in one line, without line breaks:

Finish = ambient .2 diffuse .6 specular .75 roughness .1


You can edit the resulting files with in POV-Ray too. Most of the colour and atom size attributes, parameters are declared at the beginning of the generated pov file, so you can taylor them very quickly in the POV-ray editor too.

Examples

Atom types:  any atom symbols, lone pair, dummy atom
Bond types:  1,2,3 and dotted, optionally aromatic as circles

back to POV-ray's top
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UltraMol (former MolPick)   (read & write) *

UltraMol (formerly MolPick and its sister program MolDraw) is for producing high quality drawings and pictures. It contains a simple geometry optimization module for converting the drawings to 3D structures. Lone electron pairs and dummy atoms are not allowed. The output file contains atom colours (the last three columns of the data lines), these are the same as those used by Mol2Mol.

Bond types:  1,2,3 and 4 (aromatic)
Atom types:  natural atom types as atom numbers (1-104). Coordinates are given as integers in picometer


Molecules 3D   (read & write) *

Molecules-3D (Molecular Arts Corp., http://www.molecules.com) is offered for building, editing and visualizing 3D molecules, it can produce presentation quality graphics.

Atom types:  elemental symbols, lone pair (ep)
Bond types:  single, double, triple, resonant (aromatic) and hydrogen (weak)


SHELX (read & write) *

The crystallographic structure solution and refining program family SHELX uses this file format to input and output the data and commands. For an exact description of the file structure, consult the SHELX manual or the SHELX home page http://shelx.uni-ac.gwdg.de/

Read: Mol2Mol will read the coordinate and the anisotropy data lines (the latter will be passed to CIF files, if necessary), as well as the AFIX, HFIX, PART and RESI commands and their parameters. When moving the atom cursor in the graphics window, atom labels (atom names), possible AFIX, PART and RESI commands and their parameters are reflected in the bottom status line.

Editing a SHELX file:

Enable SHELX edit This is advisable for the advanced user only, if the changed molecule is intended to be saved in the same format (if the molecule will be saved in any other non-crystallographic format, you are free to make any changes). If Q atoms are intended to delete, prior to it switch on the SHELX Edit mode option from the main Edit menu.

To delete an atom: if it is a hydrogen atom, the corresponding AFIX nm and AFIX 0 lines will be also deleted. If an atom has several instances (PART 1, PART 2… [alternative loacations]), this is taken into consideration as well. If you should delete several Q atoms, and the SHELX edit mode is enabled

SHELX delete atoms menu Q atoms - click on the atom with the right mouse button;
- Click the Select Q atom. from the pop-up menu. The selected Q atom changes to an empty rectangle;
- Keep on selecting (or unselecting in the case of a mistake) the Q atoms;
- If all of the undesired Q atoms are selected, press again the right mouse button and choose the Delete all selected Q atoms option.
Editing of the SHELX files is a new feature partly in the experimenting phase. If you experience problems during the editing or with an edited input/output file, do not hesitate to contact the distributor or the author (mol@compuchem.com or tamasgunda@tigris.klte.hu).

Adding hydrogens: you can add hydrogens in two ways: from the Edit | Add hydrogens menu (all hydrogens in one step) or from the graphics window (one-by-one) with automatically or manually selected geometry. In each case there is an option whether you want to add the hydrogens as HFIX lines, or as real atoms. The hydrogens appear in the screen, but in the former case only the HFIX lines will added to the SHELX output file. Bear in mind that the HFIX parameters describe only a few types of hydrogens (CH, CH2, CH3, =CH2, =NH2+, -OH, amide NH, aromatic CH, sp CH). The program adds the most usual parameters (13 for CH etc), you can change them by manually editing the output file. If you add hydrogens for which SHELX has no appropriate HFIX parameters (-NH2 for example), HFIX 999 appears in the output file and the program warns.

Changing the atoms: You may change a heavy atom to another one, or a hydrogen to deuterium. Avoid of changing a heavy atom to hydrogen (this is usually nonsense), or else check the output file that HFIX and AFIX lines are OK (although Mol2Mol keeps trying to follow the changes you made).

The atoms denoted as Q (which are placed in the file after the HKLF command) are treated somewhat differently from normal atoms:
- they will be drawn as small rectangles in vector mode in order to identify them more easily;
button- to help editing, enable the Show distances of neighbours button in the toolbar. In the bottom status line their distances from the nearest neighbour atoms appear automatically. The default value of the distance limit is 1.8 Angstrom. You can change it in the second Preferences window. Yellow bonds will also emphasize these atoms;
- when converting to a POV-Ray file, the colour of lawrencium (the last element) will always be used.
No hydrogens will be added to the Q atoms in automatic mode.

When converting to other molfile formats:
! Note that if the file does not contain hydrogen atoms, an automatic upward conversion is not possible. You may change this setting in the case of inorganic molecules in the Preferences, or add hydrogens via the Edit | Add hydrogens option. If in the case of coordinative compounds single bonds appear between the metal atom(s) and the ligand, remove these prior to the adding of the hydrogens. You can add them as coordinative bonds from the graphics window later.

Write:

fract. filesThis option is available only, if the input file type was also a SHELX one. Select the Convert | X-ray option from the main menu, and SHELX from the next option window. As the input file is also used during the creation of the output file, you must use a different path and/or file name.

Every data from the input SHELX file will be copied into the output file, similarly command lines between the atom data lines. Of course, the SFAC and UNIT lines will be corrected if the molecule was edited. If the input file contains HFIX or REM HFIX lines, there is an option for REMing or un-REMing the lines. This applies only to the HFIX lines of the input SHELX file and not those added within from Mol2Mol during a previous editing. The output file contains only the coordinates and the site occupation factors, for newly added atoms the site occupation factors will be defaulted to 11.000.

If the hydrogens having been added to the molecule do not have the correct HFIX parameters, the output file will contain them as:

		HFIX 999 ! =N-H
or similarly.

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User defined free format (read & write) *

* Read:

* In this input mode you absolutely control the format of the coordinate section. First of all, you have to select how to interpret the coordinates from the Preferences 1 dialog window. Apart from rare exceptions the default setting (Cartesian coordinates in Angstrom) is to be used. Does not apply in the case of Z-matrices.


format strings Prior to the input you have to supply a format string upon which the program determines how to interpret the column data. Format strings can be created, edited, stored and retrived in the appropriate dialogs available from the Preferences 3 or Open file dialog windows.

The general format is:

[number] letter1 letter2 letter3…

For example if the data lines look like:
	2-methyl-aurenon
	23 45
	1 0x0002 –0.1326  0.3333  1.2345 charge  0.1234 CA C
	2 0x0002  0.8765  0.5432  1.3232 charge  0.0023 CB C
	3 0x0002  1.1212  0.3560  2.0002 charge –0.3434 O1 O
	…
the format string should be:

2 d d x y z d p n e

* The program automatically determines the number of atoms (the input ends at the first blank line or end of file) and builds connections. The use of labelled elemental symbols is allowed: C(1), C2B, Cl(3), S6 etc. The second character, if a letter will be regarded as part of the elemental symbol. Therefore symbols like HA or HB are not allowed. Atom, residue and chain names (n, r and c) can be maximum 4 characters long (or they will be truncated).

* Write:
* In this output mode you absolutely master the format of the coordinate section. Prior to the output you have to supply a format string upon which the program determines how to assembly the data lines. Format strings can be created, edited, stored and retrived in the appropriate dialogs available from the Preferences 3 or Save file dialog windows.

The general format is very close to those used in the C/C++ language. It is not difficult even for users without any programming practice.

* In the C/C++ language strings, integer and floating point numbers have the following format specification strings (may skip this part if it is already known to you):

     * %-Ns – where N is the minimum number of characters printed (can be omitted), - (minus sign): left align the string (can be omitted)

Thus, if the actual string is “helloworld” (the blue dots here are actually spaces):

%s outputs: helloworld
%15s ouputs: •••••helloworld
%-15s outputs: helloworld•••••

     * %-Ni – where N is the minimum number of characters printed (can be omitted), - (minus sign): left align the number (can be omitted)

Thus, if the actual number is 14:

%i outputs: 14
%5i ouputs: •••14
%-5i outputs: 14•••

     * %#N.Mf – where N is the minimum number of characters printed (includig decimal point and the - sign), M is for number of decimals

Thus, if the actual number is -28.123456789

%#f  outputs: -28.123456789
%#11.4f  ouputs: •••-28.1234

All other characters, including spaces will appear in the line exactly as they are.

* Mol2Mol uses a very similar syntactic as above but instead of s, i or f different letters are used for the different data types:

     * Integer data types:

     * Floating point number data types:      * String data types: For example if you want the output data with line numbering, the three coordinates, atom number and atom name formatted as:

line••••1•••-4.111•••-5.222••••0.333•••atom••••6••CB3
use the following formatting string:

line%5i%#9.3x%#9.3y%#9.3z••atom%5a%5n

If you want to write a Z-matrix file of the following strict format, including the partial charges as the fifth data column:

C•••••1.43450•••78.00110-121.45670••••0.1234•••8•••2•••1
Cl••••1.53450•••10.00110•••60.45670•••-0.1234•••9•••2•••1
use the following formatting string:

%-2e%#10.4k0%#10.4l0%#10.4m0%#10.4p%4u%4v%4w

* Optionally you may add numbering to the atom (elemental) symbols in two different ways. The dialog window can be reached from the File menu | Preferences 3 window:

Unique number for every atom: C1, C2, C3, H4, H5, O6 etc
Unique number for each element: C1, C2, C3, H1, H2, O1 etc.
”Lettered” hydrogens: the numbers of hydrogens are derived from their parent atom, and are distinguished by the letters A, B, C, if they have a common parent atom (CH3 etc groups → H4A, H4B, H4C).


Mol2Mol (read & write) *

The own file format of Mol2Mol can be used in some special cases, for example if a file has previously been edited: special atom or bond types has been applied, rotated into a special position, some atoms were deleted or added etc. in order to convert it to a graphical file format (POV-Ray etc). In this case it is not needed to repeat the whole editing procedure, when this file is used again.


Jmol (write) *

Jmol is a free, open source molecule viewer in chemistry and biochemistry. The JmolApplet is a web browser applet that can be integrated into web pages, it is an alternative to the Chime plugin. For details see: jmol.sourceforge.net. The molecules can be used & loaded into the applet from independent molecule files, or can be used as inline structures: the molecule file is embedded into the html file as a javascript variable. The html stuff is more compact in this case, on the other hand, there’s no problem with reading the molecule files if the applet is intended to use locally.

MDL mol, HyperChem hin and Xmol xyz files can be outputted in the format of a javascript string variable. The content of the file can be directly copied into the html files.

For example an MDL mol file which looks normally:

SAURIN.MOL
  Mol2Mol 02090518193D

 60 65  0  0  0  0  0  0  0  0999 V2000
    0.2800   -3.1307   -3.3040 C   0  0  0  0  0  0  0  0  0
    1.6132   -3.5188   -3.0946 C   0  0  0  0  0  0  0  0  0
    2.3198   -3.1629   -1.9354 C   0  0  0  0  0  0  0  0  0
...
 30 58  1  0  0  0  0
 30 59  1  0  0  0  0
 31 60  1  0  0  0  0
M  END
will be outputted as:
var saurin = "SAURIN.MOL\n" +
"  Mol2Mol 02090518193D\n" +
"\n" +
" 60 65  0  0  0  0  0  0  0  0999 V2000\n" +
"    0.2800   -3.1307   -3.3040 C   0  0  0  0  0  0  0\n" +
"    1.6132   -3.5188   -3.0946 C   0  0  0  0  0  0  0\n" +
"    2.3198   -3.1629   -1.9354 C   0  0  0  0  0  0  0\n" +
…
" 30 57  1  0  0  0  0\n" +
" 30 58  1  0  0  0  0\n" +

" 30 59  1  0  0  0  0\n" +
" 31 60  1  0  0  0  0\n" +
"M  END\n"
The content of the output file can be pasted into the html file.


Gamess output files (read) *
Gamess output files are usually huge, diverse and contain a large amount of different data. They usually contain the coordinates of the molecule in several instances and in several formats. Although these can be extracted by using the marker-insertion method, now Gamess output files are automatically recognized and the structures are extracted from them. The coordinates are in Cartesian format in Bohr units, and the header of the data must possess one of the following arrangements:

ATOM      ATOMIC                      COORDINATES (BOHR)
           CHARGE         X                   Y                   Z
 C           6.0     5.0957668775       -0.1143779870       -1.3169314490
 C           6.0     3.6986987510        2.3423445736       -0.3707992407
 N           7.0     1.3485413555        1.4194685903       -1.3614980552
...
or in Ångtrom units formatted as:
COORDINATES OF ALL ATOMS ARE (ANGS)
   ATOM   CHARGE       X              Y              Z
 ------------------------------------------------------------
 C           6.0   1.3219571966   0.2493024249  -0.0000042451
 C           6.0   0.0094806504  -0.5687502291  -0.0000008599
...
All of the structures will be captured. The output file resulting from a minimization job may contain dozens of structures, the last one contains the final result. If atomic charges are present (Mulliken charges) they will also be extracted. If they occur more than once the last occurance will be used.


Gaussian 98 and 03 output files (read) *
Gaussian output files are usually huge, diverse and contain a large amount of different data. They usually contain the coordinates of the molecule in several instances and in several formats. Although these can be extracted by using the marker-insertion method, now the Gaussian 98 or 03 output files are automatically recognized and the structures are extracted from them if: Cartesian coordinates are used (this is the general case, if not changed intentionally) the structural data are preceeded with 'standard orientation' or 'input orientation' and the headers have the following structure:

                         Standard orientation:
 ---------------------------------------------------------------------
 Center     Atomic     Atomic              Coordinates (Ångstroms)
 Number     Number      Type              X           Y           Z
 ---------------------------------------------------------------------
    1          6             0        0.755142    2.196646    0.003540
    2          6             0       -0.595458    1.506524   -0.027132
    3          6             0       -0.783111    0.172674    0.040369
or
                         Input orientation:
 ---------------------------------------------------------------------
 Center     Atomic     Atomic              Coordinates (Ångstroms)
 Number     Number      Type              X           Y           Z
 ---------------------------------------------------------------------
    1          6             0        0.755142    2.196646    0.003540
    2          6             0       -0.595458    1.506524   -0.027132
    3          6             0       -0.783111    0.172674    0.040369
There might be many structures in the file, for example the results of a stepwise geometry optimization. When prompted, select the last file from the list box. If Mulliken or total atomic charges are present, they will also be extracted.


Q-Chem input file (read & write) *

* Read:

Q-Chem is an ab initio electronic structure program which brings together a variety of advanced computational methods and tools (http://www.q-chem.com/). Q-Chem input files are automatically recognized by Mol2Mol and the structural info is grabbed and displayed.

The coordinate section of the input file is marked by the $molecule keyword and ther input is ended by the $end keyword. The following formats are supported:

Cartesian coordinates with atomic symbols or numbers:
$molecule
0 1
8 0.000000 0.000000 -0.212195
1 1.370265 0.000000 0.848778
1 -1.370265 0.000000 0.848778
$end

$molecule
0 1
O 0.000000 0.000000 -0.212195
H 1.370265 0.000000 0.848778
H -1.370265 0.000000 0.848778
$end
Z-matrices with atomic symbols or numbers, with/without variables (parameters). When atomic numbers are used, atom connectivities are referred by line numbers:
$molecule
0 1
O1
O2 O1 1.5
H1 O1 1.0 O2 120.0
H2 O2 1.0 O1 120.0 H1 180.0
$end


$molecule
0 1
O1
O2 O1 OO
H1 O1 HO O2 HOO
H2 O2 HO O1 HOO H1 HOOH

OO=1.5
HOO =120.0
HO = 1.0
HOOH= 180.0
$end


$molecule
0 1
8
8 1 1.5
1 1 1.0 2 120.0
1 2 1.0 1 120.0 3 180.0
$end
Mol2Mol will automatically recognize the format.
* Write:
* In the form of Z-matrix with symbolics:

Select the Convert | Z-matrix main menu option and then Q-Chem from the Z-matrix dialog window.

* In the form of Cartesian coordinates:

Select the Convert | Cartesian main menu option and then Q-Chem from the Cartesian dialog.


Gamess input file (read & write) *

* Read:

the $CONTRL and $DATA tokens are used for recognizing the coordinate section. In the $CONTRL line the COORD=CART or ZMT or ZMTMPC switch must be present. To recognize the type of element, the 2nd column is used (atomic number). For more details consult the Gamess documentation.
$CONTRL COORD=CART UNITS=ANGS SCFTYP=ROB3LYP RUNTYP=OPTIMIZE $END
$BASIS GBASIS=31 NAUSS=6 NDFUNC=1 POLAR=1 $END
$DATA
any remark or name of the molecule
cnv naxis=6        // if symmetry is C1 the next empty line is absent

C1    6.0     1.40304   0.00000   0.00000
C2    6.0     0.70011   1.21751   0.00000
C3    6.0    -0.68795   1.21751   0.00000
...
$END


$CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE COORD=ZMT ICHARG=-1 $END
$SYSTEM TIMLIM=5 MEMORY=200000 $END
$BASIS  GBASIS=PM3 $END
$DATA
Silyl anion...comparison of semiempirical models
Cnv 3

Si
H  1  rSiH
H  1  rSiH  2 aHSiH
H  1  rSiH  2 aHSiH  3   aHSiH  -1

rSiH=1.15
aHSiH=110.0
$END
* Write:
* In the form of Z-matrix with symbolics:

Select the Convert | Z-matrix main menu option and then Gamess from the Z-matrix dialog window.

* In the form of Cartesian coordinates:

Select the Convert | Cartesian main menu option and then Gamess from the Cartesian dialog.


Turbomol input and output files (read) *

Turbomol is a quantum chemistry program package for ab initio electronic structure calculations (Prof. Ahlrichs et al., University of Karlsruhe, http://www.cosmologic.de/turbomole.html)

* Input file:

Mol2Mol will grab and input the coordinates between the %coord and %end or $coord and $end keywords. According to the options after the %coord keyword the coordinates may appear in three different formats, Mol2Mol will recognize them.

* MXYZ format (default). The coordinates are in a.u.:
%coord tmxyz
     .00000000000000     -2.68300008773804       .00000000000000  c   
     .00000000000000     -4.74300003051758       .00000000000000  h   
...
%end
* XYZ format:
%coord xyz
3
Energy = -76.46516801323
O     0.0000000    0.0000000   -0.0668805
H    -0.7658756    0.0000000    0.5307937
H     0.7658756    0.0000000    0.5307937 
%end
*Gaussian Z-matrix format:
%coord gauzmat
  o
  h  1 b1 
  h  1 b2  2 a1

b1 0.95
b2 0.95
a1 109
%end
Mol2Mol will automatically recognize the format.
* Output file:
The Turbomole/Cosmo output format is supported, which contains the coordinates in Insight format. The coordinates between the !DATE and END keywords are read and interpreted:
$cosmo_info
…
!BIOSYM archive 3
PBC=OFF
coordinates from TURBOMOLE/COSMO calculation
!DATE  
N1       0.000082499    0.000068354    0.365302084 TURB 1      n       N   0.000
C1      -0.003323548   -1.392400135   -0.090326283 TURB 1      c       C   0.000
...
end
end