babel

Programmname:
babel
Kurzbeschreibung:
Molecular Modeling Dateiformat-Interkonversion
Version:
1.6
Voraussetzungen:
-
Aufruf:
babel -m (interaktiv menügesteuert)
babel [-v] -iinput-type infile [keywords] -ooutput-type outfile [keywords2]
Information:
(Usage note beim Aufruf babel ohne Parameter)
README (s.u.)
Ansprechpartner:
Burkhard Kirste

Aus dem "Readme"

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

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

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.

PLEASE REGISTER

We don't want any money for Babel (unless of course you insist), but we would like to know who has a copy so that we can notify people about updates and bug fixes.

You can register by sending e-mail to babel@mercury.aichem.arizona.edu and letting us know the following: who you are, where you are, what platform you're running Babel on, which file conversions you commonly use.

We are very open to suggestions. If there's anything you like or don't like about the program please let us know. Also if there are file formats you would like to see supported let us know.


Thanks for downloading this copy of babel. With this program we hope to implement a general framework for converting between file formats used for molecular modeling.

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] -iitype infile [keywords] -oout_type outfile [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.

        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
        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

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

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

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 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:

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 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

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

When converting a multi structure file it is necessary to supply a keyword after the input file name. This keyword specifies the number of files to extract from the iput file. The keyword can be either a number or the word all. Hopefully the examples below will make this a little more clear.

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 -op mols.pdb

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

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

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 -imacmod mols.out "1-5" -oai 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.

To add hydrogens to 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 -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 -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 alot 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 (not the -imaccs2) flag. Here are a couple of examples of how to convert NCI 3D.

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

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 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 -imaccs nci3d.mol "1-500" -omol2 CON > nci3d.mol2

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

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

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.

To read a MacMolecule file named foo.bar where X is substituted for Cl and Y is substituted 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

The user can supply a keyword to indicate the viewing axis for the ChemDraw projection. To convert an XYZ file named test.xyz to a ChemDraw file named test.cdx with the view down the y axis the user would type:

babel -ixyz 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
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 coordinates Babel will use the input coordinates. If Babel uses the input coordinates 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 -ox 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

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

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

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

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

    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.

Other Stuff

Current Limitations

Macromodel - bond orders are not always correctly assigned for conjugated pi systems.

PDB files - When reading PDB files Babel assigns bonds by examining interatomic distances and assigning a bond where the interatomic distance is less than the sum of the atoms covalent 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

Noone 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 babel@mercury.aichem.arizona.edu 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.

Credit Where Credit is Due

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

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 - pat@mercury.aichem.arizona.edu).

Please Write

We would really appreciate any and all input from babel users. Please send comments, praise, flames, and job offers :-) to babel@mercury.aichem.arizona.edu

Have fun,

Pat Walters, Chief Cook and Bottle-Washer

Source

Babel is available by anonymous FTP from:

joplin.biosci.arizona.edu:/pub/Babel

Or from the mirror site ftp.fu-berlin.de:

ftp.fu-berlin.de:/science/chemistry/babel


General part and formatting of README: Burkhard Kirste, Wolfgang Dreißig, 1994/04/20, 1996/06/29, 1999/02/15