Dream 44/Amiga_Dream_44.iso/Amiga/pov/utils/pdb2pov_121.lha/babel.doc

Text File | 1994-01-23 | 12KB | 339 lines

          Babel version 1.03 Copyright (C) 1992,1993,1994
                  by
              Pat Walters and Matt Stahl

            Dolata Research Group
               Department of Chemistry
            University of Arizona
               Tucson, AZ 85721
           [e-mail]




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 [e-mail] 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.
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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.  This is the first version of the manual, and
we are sorry to say that it's rather meager.  However, the program is very
easy to use and we're sure that by scanning over these few pages you'll
be babbling away before you know it.   This manual is divided into 3
sections.

I. Installation
II. Using Babel
III. Other Stuff

I. INSTALLATION
UNIX INSTALLATION
Installation is very simple.

1. Special Instructions - Unless you have a Sun Workstaion with an old
Sabre C compiler (or other non-ansi C compiler) or a Dec machine running
Ultrix goto step 2.

SUN WORKSTATIONS WITH THE OLD (NON-ANSI) SABRE C COMPILER
If you have a Sun workstation with the old Sabre C compiler or another
non-ANSI C-compiler you must use gcc to compile babel. If you are using
gcc to compile babel, change line 10 in the makefile from

CC          = cc

to

CC          = gcc

DEC STATIONS RUNNING ULTRIX - If you have gcc follow the instructions above
to use gcc as the compiler.  Otherwise change line 1 in the Makefile from

CFLAGS        = -O

to

CFLAGS        = -O -ULTRIX

2. Make the program by typing make.
3. Set the environment variable BABEL_DIR to point to the directory
where the files types.lis and elements.lis are stored.
i.e. If the files are in /usr/local/babel type the following

setenv BABEL_DIR /usr/local/babel

If you plan to use babel frequently then you will probably want to
place the line above in your .cshrc file.


II. 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<itype> <infile> [keywords] -o<out 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.

    ac -- Mopac Cartesian file
    ao -- Mopac Output file
    ai -- Mopac Internal file
    c -- CSD GSTAT file
    cf -- CSD CSSR file
    f -- Free Form Fractional file
    k -- Macromodel file
    micro -- Micro World file
    mo -- MM2 Ouput file
    p -- PDB file
    t -- Alchemy file
    x -- XYZ file
    prep -- AMBER PREP file
    molin -- MOLIN file
    boog -- Boogie file
    caccrt -- Cacao Cartesian file
    macmol -- Mac Molecule file
    c3d1 -- Chem 3D Cartesian 1 file
    c3d2 -- Chem 3D Cartesian 2 file
    bs -- Ball and Stick file
    g -- Gaussian Z-Matrix file
    gauout -- Gaussian Output file
    gamout -- GAMESS Output file
    mmads -- MMADS file
    shelx -- ShelX file
    mol2 -- Sybyl Mol2 file
    fdat -- CSD FDAT file
    charmm -- CHARMm file
    mdl -- MDL Molfile file

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

    diag -- DIAGNOTICS file
    ac -- Mopac Cartesian file
    ai -- Mopac Internal file
    g -- Gaussian Z-matrix file
    gcart -- Gaussian Cartesian file
    i -- IDATM file
    k -- Macromodel file
    macmol -- Mac Molecule file
    micro -- Micro World file
    mi -- MM2 Input file
    mo -- MM2 Ouput file
    p -- PDB file
    report -- Report file
    t -- Alchemy file
    caccrt -- Cacao Cartesian file
    x -- XYZ file
    bs -- Ball and Stick file
    c3d1 -- Chem 3D Cartesian 1 file
    c3d2 -- Chem 3D Cartesian 2 file
    d -- ChemDraw Connection Table file
    mdl -- MDL Molfile file
    gamin -- Gamess Input file
    mmads -- MMADS file
    mol2 -- Sybyl Mol2 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.

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 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 -ik benzene.dat -d -ox benzene.new

MULTI-STRUCTURE FILES
Babel will currently read multi-structure files produced by Macromodel.
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 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 -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 5 -oai mols.int
The output files would be written as mols1.int, mols2.int. etc.

It is sometimes necessary to convert a mulit-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

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 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
The user can supply a keyword to indicate the viewing axis for the
ChemDraw projection by supplying a keyword.  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 -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---
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 -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 coordiantes named coords.in the user would type:
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 Coordiantes.


III. 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 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
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
[e-mail] 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 - [e-mail]).

PLEASE WRITE
We would really appreciate any and all input from babel users.  Please
send comments, praise, flames, and job offers :-) to
[e-mail]

Have fun,

Pat Walters
Chief Cook and Bottle-Washer