Babel version 1.1 Copyright (C) 1992,1993,1994
				  by
		      Pat Walters and Matt Stahl

			Dolata Research Group
		       Department of Chemistry
			University of Arizona
			   Tucson, AZ 85721
		   babel@mercury.aichem.arizona.edu

About Babel

Babel is avialiable via anonymous ftp from joplin.biosci.arizona.edu in pub/Babel (ftp).

Babel is capable of assigning hybridization, bond order, and connectivity when these elements are not present in the input file.

Babel has the ability to add and delete hydrogens from any file format.

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.

Table of contents

1. File Types
2. Using Babel
3. Z-matrix renumbering
4. Multi-structure files
5. Hydrogen addition/deletion
6. Converting the NCI database
7. Details for MacMolecule, ChemDraw, Gamess & Quanta files
8. Current limitations
9. Coming attractions
10. Reporting bugs
11. Credits

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                Feature                  Free Form Fractional     
GAMESS Output            Gaussian Z-Matrix        Gaussian Output          
Hyperchem HIN            MDL Isis                 Mac Molecule             
Macromodel               Micro World              MM2 Input                
MM2 Ouput                MM3                      MMADS                    
MDL MOLfile              MOLIN                    Mopac Cartesian          
Mopac Internal           Mopac Output             PC Model                 
PDB                      Quanta                   ShelX                    
Spartan                  Spartan Semi-Empirical   Spartan Mol. Mechanics   
Sybyl Mol                Sybyl Mol2               Conjure                  
Maccs 2d                 Maccs 3d                 UniChem XYZ              
XYZ                      XED                      

Output file types

Alchemy                  Ball and Stick           Batchmin Command         
Cacao Cartesian          Cacao Internal           CAChe MolStruct          
Chem3D Cartesian 1       Chem3D Cartesian 2       ChemDraw Conn. Table     
Conjure                  Conjure Template         CSD CSSR                 
Feature                  Fenske-Hall ZMatrix      Gamess Input             
Gaussian Cartesian       Gaussian Z-matrix        Gaussian Z-matrix tmplt  
Hyperchem HIN            Icon 8                   IDATM                    
Mac Molecule             Macromodel               Micro World              
MM2 Input                MM2 Ouput                MM3                      
MMADS                    MDL Molfile              Mopac Cartesian          
Mopac Internal           PC Model                 PDB                      
Report                   Spartan                  Sybyl Mol                
Sybyl Mol2               MDL Maccs file           XED                      
UniChem XYZ              XYZ                      

USING BABEL

The menu interface can be accessed by typing:

babel -m

The command line input has the following format:

babel [-v] -i [keywords] -o [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 type. The following input type codes are currently supported:

Currently supported input type codes

• t -- Alchemy file
• prep -- AMBER PREP file
• bs -- Ball and Stick 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
• c -- CSD GSTAT file
• feat -- Feature file
• f -- Free Form Fractional file
• gamout -- GAMESS Output file
• g -- Gaussian Z-Matrix file
• gauout -- Gaussian Output file
• hin -- Hyperchem HIN file
• isis -- MDL Isis file
• macmol -- Mac Molecule file
• k -- Macromodel file
• micro -- Micro World file
• mi -- MM2 Input file
• mo -- MM2 Ouput file
• mm3 -- MM3 file
• mmads -- MMADS file
• mdl -- MDL MOLfile file
• molen -- MOLIN file
• ac -- Mopac Cartesian file
• ai -- Mopac Internal file
• ao -- Mopac Output file
• pc -- PC Model file
• p -- PDB file
• quanta -- Quanta file
• shelx -- ShelX file
• spar -- Spartan file
• semi -- Spartan Semi-Empirical file
• spmm -- Spartan Mol. Mechanics file
• mol -- Sybyl Mol file
• mol2 -- Sybyl Mol2 file
• con -- Conjure file
• maccs2 -- Maccs 2d file
• maccs3 -- Maccs 3d file
• unixyz -- UniChem XYZ file
• x -- XYZ file
• xed -- XED file

The -o flag is used to set the output file type. The following output type codes are currently supported:

Currently supported output type codes

• diag -- DIAGNOTICS file
• t -- Alchemy file
• bs -- Ball and Stick file
• bmin -- Batchmin Command file
• caccrt -- Cacao Cartesian file
• cacint -- Cacao Internal file
• cache -- CAChe MolStruct file
• c3d1 -- Chem3D Cartesian 1 file
• c3d2 -- Chem3D Cartesian 2 file
• d -- ChemDraw Conn. Table file
• con -- Conjure file
• contmp -- Conjure Template file
• cssr -- CSD CSSR file
• feat -- Feature file
• fhz -- Fenske-Hall ZMatrix file
• gamin -- Gamess Input file
• gcart -- Gaussian Cartesian file
• g -- Gaussian Z-matrix file
• gotmp -- Gaussian Z-matrix tmplt file
• hin -- Hyperchem HIN file
• icon -- Icon 8 file
• i -- IDATM file
• macmol -- Mac Molecule file
• k -- Macromodel file
• micro -- Micro World file
• mi -- MM2 Input file
• mo -- MM2 Ouput file
• mm3 -- MM3 file
• mmads -- MMADS file
• mdl -- MDL Molfile file
• ac -- Mopac Cartesian file
• ai -- Mopac Internal file
• pc -- PC Model file
• p -- PDB file
• report -- Report file
• spar -- Spartan file
• mol -- Sybyl Mol file
• mol2 -- Sybyl Mol2 file
• maccs -- MDL Maccs file file
• xed -- XED file
• unixyz -- UniChem XYZ file
• x -- XYZ file

Examples

babel -imo mm2.grf -oai 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 -imo mm2.grf -oai mopac.dat "PM3 GEO-OK T=30000"

Note the use of the double quotes around the keywords.

Z-MATRIX RENUMBERING

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)
        }

I've added a new flag, "-renum" to Babel 1.1. 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

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

babel -ix myfile.xyz -renum 9 -oai 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 limitiation 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

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

Examples

babel -ik mols.out all -op mols.pdb

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 mopac internal coordinate file the user would type:

babel -ik mols.out "1-5" -oai mols.int

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

It is sometimes necessary to convert a multi-structure Macromodel file into a multi-structure file of another type. This can be a handy way of viewing Macromodel movies with the Xmol program. Babel accomplishes this by sending the output to the console using the output file name CON (note the use of uppercase letters). Once again this is better explained by an example. To convert all the structures in a multi-structure Macromodel file called mols.out to a multi-structure XYZ file called mols.xyz the user would type:

babel -ik mols.out all -ox CON > mols.xyz

HYDROGEN ADDITION/DELETION

Examples

babel -icf input.cssr -h -oai 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 -ik benzene.dat -d -ox benzene.new

CONVERTING THE NCI DATABASE

Babel is capable of reading the NCI database using the -imaccs3 (not the -imaccs2 ) flag. Here are a couple of examples of how to convert NCI 3D.

Examples

babel -imaccs3 nci3d.mol all -omol2 CON > 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 -imaccs3 nci3d.mol all -omol2 CON > 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 -imaccs3 nci3d.mol "1-500" -omol2 CON > nci3d.mol2

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

babel -h -imaccs3 nci3d.mol "501-1000" -omol2 CON > 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 -imaccs3 nci3d.mol "1-100" -ok nci.dat

Details for MacMolecule, ChemDraw, Gamess & Quanta files

MACMOLECULE FILES

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 -omo bar.baz

CHEMDRAW FILES

babel -ix test.xyz -od 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

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 -ox exam01.xyz

GAMESS Input Files

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

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

babel -ix coords.xzy -ogamin coords.in cart

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

babel -ix coords.xzy -ogamin coords.in zmt

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

GAUSSIAN FILES

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 -ox CON > 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 -ox file.xyz

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

   babel -igauout file.out last -ox 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

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 a lot of strange atom types (i.e. Carbon with 2 Fluorines attached) which don't translate easily to the hybridized types we use. Second, I found that the bonding information found in the Quanta files was not always 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

PDB files: When reading PDB files Babel assigns bonds 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.

COMING ATTRACTIONS

REPORTING BUGS

CREDIT WHERE CREDIT IS DUE

PLEASE WRITE

Have fun,

Pat Walters
Chief Cook and Bottle-Washer