Babel Notes

Babel is a program designed to interconvert a number of file formats currently used in molecular modeling. It is capable of assigning hybridization, bond order, and connectivity when these elements are not present in the input file. It also has the ability to add and delete hydrogens from any file format. The program is available for Unix (AIX, Ultrix, Sun-OS, Convex, SGI, Cray, Linux), MS-DOS, and on Macs running at least System 7.0.

(The notes were produced from the README.1ST file in the Babel distribution with minor change.)

Babel version 1.6 Copyright (C) 1992-1996
by
Pat Walters and Matt Stahl

This software is provided on an "as is" basis, and without warranty of any kind, including but not limited to any implied warranty of merchantability or fitness for a particular purpose.

In no event shall the authors or the University of Arizona be liable for any direct, indirect, incidental, special, or consequential damages arising from use or distribution of this software. The University of Arizona also shall not be liable for any claim against any user of this program by any third party.

• What's new
• File types
• Using Babel
• Z-matrix renumbering
• Multi-structure files
• Hydrogen addition/deletion
• Converting the NCI database
• MacMolecule files
• ChemDraw file
• Gamess file
• Gaussian file
• Quanta file
• Current limitations
• Coming attractions
• Reporting bugs
• Credits

What's New

• SMILES support - thanks Simon Kilvington
• Gaussian 94 support
• Command line arguments have changed a bit. See the section below on multi-structure files.

File Types

Input file types:

Alchemy                  AMBER PREP               Ball and Stick
Biosym .CAR              Boogie                   Cacao Cartesian
Cambridge CADPAC         CHARMm                   Chem3D Cartesian 1
Chem3D Cartesian 2       CSD CSSR                 CSD FDAT
CSD GSTAT                Dock Database            Dock PDB
Feature                  Free Form Fractional     GAMESS Output
Gaussian Output          Gaussian Z-Matrix        Gaussian 92 Output
Gaussian 94 Output       GAMESS Output (A)        GROMOS96 (nm)
Hyperchem HIN            MDL Isis (SDF)           M3D
Mac Molecule             Macromodel               Micro World
MM2 Input                MM2 Ouput                MM3                      
MMADS                    MDL MOLfile              MOLIN
Mopac Cartesian          Mopac Internal           Mopac Output             
PC Model                 PDB                      PS-GVB Input
PS-GVB Output            Quanta MSF               Schakal
ShelX                    SMILES                   Spartan
Spartan Semi-Empirical   Spartan Mol. Mechanics   Sybyl Mol
Sybyl Mol2               Conjure                  UniChem XYZ
XYZ                      XED

Output file types

Alchemy                  Ball and Stick           BGF
Batchmin Command         DOCK 3.5 box             Cacao Cartesian
Cacao Internal           CAChe MolStruct          Chem3D Cartesian 1
Chem3D Cartesian 2       ChemDraw Conn. Table     Dock Database
Wizard                   Conjure Template         CSD CSSR
Dock PDB                 Feature                  Fenske-Hall ZMatrix
Gamess Input             Gaussian Cartesian       Gaussian Z-matrix
Gaussian Z-matrix tmplt  GROMOS96 (A)             GROMOS96 (nm)
Hyperchem HIN            Icon 8                   IDATM
MDL Isis SDF             M3D                      Mac Molecule             
Macromodel               Micro World              MM2 Input                
MM2 Ouput                MM3                      MMADS                    
MDL Molfile              MolInventor              Mopac Cartesian          
Mopac Internal           MSI Quanta CSR           PC Model                 
PDB                      PS_GVB Z-Matrix          PS-GVB Cartesian         
Report                   SMILES                   Spartan                  
Sybyl Mol                Sybyl Mol2               MDL Maccs                
Torsion List             Tinker XYZ               UniChem XYZ              
XYZ                      XED

Using Babel

The babel program may be invoked using command line options or menus.

The menu interface can be accessed by typing:

 

babel -m

 

The command line input has the following format:

 

babel [-v] -i<in-type> <in-file> ["keywords1"] -o<out-type> <out-file> ["keywords2"]

 

All arguments surrounded by [] are optional.

The -v flag is optional and is used to produce verbose output.

The -i flag is used to set the input file type.

The following input type codes are currently supported:

	alc ------ Alchemy file
	prep ----- AMBER PREP file
	bs ------- Ball and Stick file
	bgf ------ MSI BGF file
	car ------ Biosym .CAR file
	boog ----- Boogie file
	caccrt --- Cacao Cartesian file
	cadpac --- Cambridge CADPAC file
	charmm --- CHARMm file
	c3d1 ----- Chem3D Cartesian 1 file
	c3d2 ----- Chem3D Cartesian 2 file
	cssr ----- CSD CSSR file
	fdat ----- CSD FDAT file
	gstat ---- CSD GSTAT file
	dock ----- Dock Database file
	dpdb ----- Dock PDB file
	feat ----- Feature file
	fract ---- Free Form Fractional file
	gamout --- GAMESS Output file
	gzmat ---- Gaussian Z-Matrix file
	gauout --- Gaussian 92 Output file
	g94 ------ Gaussian 94 Output file
	gr96A ---- GROMOS96 (A) file
	gr96N ---- GROMOS96 (nm) file
	hin ------ Hyperchem HIN file
	sdf ------ MDL Isis SDF file
	m3d ------ M3D file
	macmol --- Mac Molecule file
	macmod --- Macromodel file
	micro ---- Micro World file
	mm2in ---- MM2 Input file
	mm2out --- MM2 Output file
	mm3 ------ MM3 file
	mmads ---- MMADS file
	mdl ------ MDL MOLfile file
	molen ---- MOLIN file
	mopcrt --- Mopac Cartesian file
	mopint --- Mopac Internal file
	mopout --- Mopac Output file
	pcmod ---- PC Model file
	pdb ------ PDB file
	psin ----- PS-GVB Input file
	psout ---- PS-GVB Output file
	msf ------ Quanta MSF file
	schakal -- Schakal file
	shelx ---- ShelX file
	smiles --- SMILES file
	spar ----- Spartan file
	semi ----- Spartan Semi-Empirical file
	spmm ----- Spartan Mol. Mechanics file
	mol ------ Sybyl Mol file
	mol2 ----- Sybyl Mol2 file
	wiz ------ Conjure file
	unixyz --- UniChem XYZ file
	xyz ------ XYZ file
	xed ------ XED file

The -o flag is used to set the output file type.

The following output type codes are currently supported:

        diag ----- DIAGNOTICS file
        alc ------ Alchemy file
        bs ------- Ball and Stick file
        bgf ------ BGF file
        bmin ----- Batchmin Command file
        box ------ DOCK 3.5 box file
        caccrt --- Cacao Cartesian file
        cacint --- Cacao Internal file
        cache ---- CAChe MolStruct file
        c3d1 ----- Chem3D Cartesian 1 file
        c3d2 ----- Chem3D Cartesian 2 file
        cdct ----- ChemDraw Conn. Table file
        dock ----- Dock Database file
        wiz ------ Wizard file
        contmp --- Conjure Template file
        cssr ----- CSD CSSR file
        dpdb ----- Dock PDB file
        feat ----- Feature file
        fhz ------ Fenske-Hall ZMatrix file
        gamin ---- Gamess Input file
        gcart ---- Gaussian Cartesian file
        gzmat ---- Gaussian Z-matrix file
        gotmp ---- Gaussian Z-matrix tmplt file
        gr96A ---- GROMOS96 (A) file
        gr96N ---- GROMOS96 (nm) file
        hin ------ Hyperchem HIN file
        icon ----- Icon 8 file
        idatm ---- IDATM file
        sdf ------ MDL Isis SDF file
        m3d ------ M3D file
        macmol --- Mac Molecule file
        macmod --- Macromodel file
        micro ---- Micro World file
        mm2in ---- MM2 Input file
        mm2out --- MM2 Ouput file
        mm3 ------ MM3 file
        mmads ---- MMADS file
        mdl ------ MDL Molfile file
        miv ------ MolInventor file
        mopcrt --- Mopac Cartesian file
        mopint --- Mopac Internal file
        csr ------ MSI Quanta CSR file
        pcmod ---- PC Model file
        pdb ------ PDB file
        psz ------ PS-GVB Z-Matrix file
        psc ------ PS-GVB Cartesian file
        report --- Report file
        smiles --- SMILES file
        spar ----- Spartan file
        mol ------ Sybyl Mol file
        mol2 ----- Sybyl Mol2 file
        maccs ---- MDL Maccs file
        torlist -- Torsion List file
        tinker --- Tinker XYZ file
        unixyz --- UniChem XYZ file
        xyz ------ XYZ file
        xed ------ XED file

Note:  The input and output type codes used in version 1.6 are different from that in version 1.1g (the previous version installed in the IU MolViz server). For example, the type code for PDB files is pdb in version 1.6 but p in version 1.1g (see the file type code list for version 1.1g). Typing the babel command without any arguments will display the file type codes used in the current version.

Example:

To convert an MM2 output file named mm2.grf to a MOPAC internal coordinate input file named mopac.dat the user would enter:

 

babel -imm2out mm2.grf -omopint mopac.dat

 

To perform the above conversion with the keywords PM3 GEO-OK T=30000 in the file mopac.dat the user would enter:

 

babel -imm2out mm2.grf -omopint mopac.dat "PM3 GEO-OK T=30000"

 

Note the use of the double quotes around the keywords.

 

If CON (note the use of uppercase letters) is used as the output file name, the output will be send to the console (screen), for example:

 

babel -imm2out mm2.grf -omopint CON

Z-Matrix Renumbering

I have received mail from a number of people who have complained that the Z-matrix created by Babel contains very long "bonds" (often 5 to 10 angstroms). This is not a bug in the Cartesian to internal algorithm. It is actually brought about by a poorly numbered structure.

The Cartesian to internal algorithm goes kind of like this :

        put atom 1 at the origin
        for i = 2 to num_atoms
         {
          find the closest atom with atom number < i
          call that atom NA(i)
         }

If atoms are not numbered properly you end up with very long bonds. Having these "bonds" in your Z-matrix tends to create all sorts of problems during geometry optimization.

I've added a new flag, "-renum" to Babel. If this flag is used, Babel will attempt to renumber the structure so that the Z-matrix is contiguous.

Renumbering in Babel 1.1 is accomplished using the -renum flag. There are two ways to this. If you use -renum by itself, Babel will use atom 1 in the input structure as atom 1 in the Z-matrix. If you use -renum X where X is an integer, Babel will use atom X as atom 1 in the Z-matrix.

Examples:

babel -ixyz myfile.xyz -renum -omopint myfile.dat "AM1 MMOK T=30000"

 

will create a MOPAC input file with atom 1 from myfile.xyz as atom 1 in myfile.dat.

 

babel -ixyz myfile.xyz -renum 9 -omopint myfile.dat "AM1 MMOK T=30000"

 

will create a MOPAC input file with atom 9 from myfile.xyz as atom 1 in myfile.dat.

There is currently one limitation to the -renum flag. The file must be contiguous. The method won't currently work for bimolecular complexes or anything like that. I'll try and fix this up in the near future.

If you run into any problems with this, please don't hesitate to contact me.

Multi-structure Files

Most file formats are now supported as multi-structure. With this type of file, the user has two output options

• produce one output file for each structure in the file
• produce a multi-structure output file.

When converting a multi structure file it is sometimes necessary to supply a keyword after the input file name. This keyword specifies the number of files to extract from the input file. Hopefully the examples below will make this a little more clear.

Example:

To extract all the structures from a multi-structure Macromodel file called mols.out and write the structures as pdb files the user would type:

 

babel -imacmod mols.out all -opdb mols.pdb

 

To extract the structures into a series of single structure files use the -split keyword:

 

babel -imacmod mols.out all -opdb mols.pdb -split

 

The output files would be written as mols1.pdb, mols2.pdb, etc.

 

To extract only the first five structures from a multi-structure Macromodel file and write the structures as a MOPAC internal coordinate file the user would type:

 

babel -imacmod mols.out "1-5" -omopint mols.int

Hydrogen Addition/deletion

Babel has the ability to add and delete hydrogens from any file format. Hydrogens can be added by supplying the -h flag, hydrogens may be deleted by supplying the -d flag.

Example:

To add hydrogens a CSD fractional coordinate file called input.cssr and output the file as a MOPAC internal coordinate input file named output.add the user would type:

 

babel -icf input.cssr -h -omopint output.add

 

To delete hydrogens from a Macromodel file named benzene.dat and output the file as an XYZ file name benzene.new the user would type:

 

babel -imacmod benzene.dat -d -oxyz benzene.new

Converting the NCI Database

Now that Professor Gasteiger's group has made the NCI database available as 3D structures, I'm sure that a lot of people will be interested in converting the database to other formats. Many people people also want to add the hydrogens which are missing in the NCI 3D database.

Babel is capable of reading the NCI database using the -imaccs flag. Here are a couple of examples of how to convert NCI 3D.

Example:

If you want to convert the entire database to one huge Sybyl mol2 file, you would type the following:

 

babel -imaccs nci3d.mol -omol2 nci3d.mol2

 

If you want to convert the entire database to one huge Sybyl mol2 file and add hydrogens, you would do the following:

 

babel -h -imaccs nci3d.mol -omol2 nci3d.mol2

 

Let's say you're slightly less ambitious and you only want to look at the first 500 structures. Then you would do this:

 

babel -h -imaccs nci3d.mol "1-500" -omol2 nci3d.mol2

 

If you wanted to look at the next 500 structures you would do this:

 

babel -h -imaccs nci3d.mol "501-1000" -omol2 nci3d.mol2

 

To read the first 100 structures and output them to individual MacroModel files named nci0001.dat, nci0002.dat, nci0003.dat, etc., you would type:

 

babel -h -imaccs nci3d.mol "1-100" -omacmod nci.dat -split

MacMolecule Files

Since MacMolecule only uses single letter it is often necessary to use different names (i.e. X for Cl). The user can specify substituted atom names on the command line.

Example:

To read a MacMolecule file named foo.bar where X is substituted for Cl and Y is substitued for Cobalt and write an MM2 output type file named bar.baz the user would type:

 

babel -imacmol "X/Cl Y/Co" foo.bar -omm2out bar.baz

ChemDraw Files

The user can supply a keyword to indicate the viewing axis for the ChemDraw projection by supplying a keyword.

Example:

To convert an XYZ file named test.xyz to a ChemDraw file named test.cdy with the view down the y axis the user would type:

 

babel -ixyz test.xyz -ocdct test.cdx x

 

The default view is down the z axis. Babel will also write MDL Molfile type files which can be read by ChemDraw, ChemIntosh, ChemWindow, and Chem3D.

Gamess Files

Gamess output files

The output files are the .log files created by redirecting screen output. Babel first looks for a set of geometry optimized coordinates. If the output file does not contain geometry optimized coordiantes Babel will use the input coordiantes. If Babel uses the input coordiantes it will convert from Bohr to Angstroms.

To read a GAMESS output file named exam01.log and convert it to an XYZ file named exam01.xyz the user would type:

 

babel -igamout exam01.log -oxyz exam01.xyz

Gamess input files

Babel is capable of creating three types of GAMESS input files

• COORD=CART Cartesian Coordinates
• COORD=ZMAT Gaussian Style Z-matrix
• COORD=ZMTPC MOPAC Style Z-matrix

Babel does not calculate the point group for you. You'll have to pull out your copy of Cotton and insert that manually. You'll also have to specify your own $SYSTEM, $BASIS, $SCF, $GUESS, etc. cards.

The type of input file is controlled by specifying a keyword on the Babel command line. The keywords are

• cart ------ Cartesian
• zmt ------ Gaussian style Z-matrix
• zmtmpc -- MOPAC style Z-matrix Exapmle:

Example:

 

To read an xyz file named coords.xyz and convert it to a GAMESS input file in Cartesian coordiantes named coords.in the user would type:

 

babel -ixyz coords.xyz -ogamin coords.in cart

 

To do the same conversion by have the GAMESS input in Gaussian Z-matrix style the user would type:

 

babel -ixyz coords.xyz -ogamin coords.in zmt

 

If no keyword is specified the input file will be in Cartesian Coordiantes.

Gaussian Files

NOTE : The output file format for Gaussian94 in different from that used by previous versions of Gaussain. Use the -g94 flag to read Gaussian94 output files.

Babel 1.6 features a number of improvements aimed at the Gaussian user.

1. A (hopefully) bulletproof Gaussian reader.
2. A new reader for gaussian output files which reads all the steps from a minimization. These steps can then be written to a multistructure file which can be animated with X-mol or whatever. To extract all the steps from a Gaussian output file into a single muti structure XYZ file you would do this:

    

   babel -igauout file.out all -oxyz file.xyz

    

   To extract all the steps from a Gaussian output file into a series of files called file0001.xyz, file0002.xyz, etc. You would do this:

    

   babel -igauout file.out all -oxyz file.xyz -split

    

   To extract only the last step from a Gaussian output file you would do this:

    

   babel -igauout file.out last -oxyz file.xyz

    

3. We added the facility to define the header information for your Gaussian files. To do this you need to have a file with the header info in either the current directory (checked first) or the directory pointed to by the BABEL_DIR environment variable (checked second). If the header file isn't present Babel just puts in its default header information. This can be handy if you constantly use the same basis sets and run the same sorts of jobs. There is a sample gauss.hdr in the archive.

Quanta Files

Quanta files are binary and different systems use different binary representations (big endian vs. little endian). So, if you are going to use Babel on a Quanta file you should run Babel on the same type of machine which created the Quanta file.

I made a few concessions with this file format. First, I just translated the Quanta atom types to element types and let Babel assign hybridizations. Quanta has alot of strange atom types (i.e. Carbon with 2 Flourines attached) which don't translate easily to the hybidizized types we use. Second, I found that the bonding information found in the Quanta files was not alway reliable so I had Babel assign connectivities.

There is a file called quanta.lis which should be kept in the directory pointed to by BABEL_DIR. This file contains the numeric quanta type and corresponding element type. If anything is missing or incorrect you can just edit this file and fix it.

Current Limitations

Macromodel

Bond orders are not always correctly assigned for conjugated pi systems.

 

PDB files

When reading PDB files Babel assigns bonds are examining interatomic distances and assigning a bond where the interatomic distance is less than the sum of the atoms convalent radii. There is code in read_pdb.c to read connections specified in CONECT records, but this code is commented out. We did this because a number of files available from Brookhaven have CONECT records specified for only a few of the bonds in the molecule. We realize that we could determine connectivity in the PDB file by looking at atom ids and residue types, but we have put this in yet. This feature will probably be added soon. If you would like to use the explicit CONECT records in a PDB file see Appendix A. When writing PDB files all residue types are assigned as UNK.

Reporting Bugs

No one is perfect, and we're sure that there are still a few glitches in this program. If you happen to find such a glitch please send a mail message to pwalters@vpharm.com describing the nature of the problem. If possible please include the input file so we can use it to determine the cause of the problem.

Coming Attractions

We consider Babel to be a constantly evolving program. Hopefully modules to handle new file formats will be contributed and the program will become useful to an even wider range of chemists. We currently have a number of additions to Babel underway at the U of A. Among these are:

1. A real users manual
2. A developers guide which will assist programmers in creating new modules (Actually I have finished a draft of the Babel Developers Guide. If you'd like a copy send me some mail - pwalters@vpharm.com.

Credit Where Credit is Due

Babel began it's life a program called convert written by Ajay Shah. Babel in its current form was written by Pat Walters and Matt Stahl.