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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
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.
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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.
Babel will read the following 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 Free Form Fractional GAMESS Output
Gaussian Z-Matrix Gaussian Output Hyperchem HIN
Mac Molecule Macromodel Micro World
MM2 Input MM2 Ouput MM3
MMADS MDL MOLfile MOLIN
Mopac Cartesian Mopac Internal Mopac Output
PDB Quanta ShelX
Spartan Sybyl Mol Sybyl Mol2
XYZ
Babel will write the following file types :
Alchemy Ball and Stick Cacao Cartesian
CAChe MolStruct Chem3D Cartesian 1 Chem3D Cartesian 2
ChemDraw Conn. Table CSD CSSR Gamess Input
Gaussian Cartesian Gaussian Z-matrix Hyperchem HIN
IDATM Mac Molecule Macromodel
Micro World MM2 Input MM2 Ouput
MM3 MMADS MDL Molfile
Mopac Cartesian Mopac Internal PDB
Report Spartan Sybyl Mol
Sybyl Mol2 XYZ
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
A. Unix Installation
B. DOS Installation
II. Using Babel
III. Other Stuff
I. INSTALLATION
--------------------------UNIX INSTALLATION-----------------------------
NOTE : If you downloded either sun-babel-1.0X.tar.Z or sgi-babel-1.0X.tar.Z
please skip directly to step 3.
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 -DULTRIX
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.
---------------------------DOS INSTALLATION------------------------------
1. Create a subdirectory for babel on your hard disk.
We will assume that you called the directory C:\BABEL.
2. Copy the files babel.exe, element.lis, and types.lis
into this directory.
3. Put the following line in your autoexec.bat file
SET BABEL_DIR=C:\BABEL
4. You're all set, have fun.
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 [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 types
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
f -- Free Form Fractional file
gamout -- GAMESS Output file
g -- Gaussian Z-Matrix file
gauout -- Gaussian Output file
hin -- Hyperchem HIN 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
molin -- MOLIN file
quanta -- Quanta file
ac -- Mopac Cartesian file
ai -- Mopac Internal file
ao -- Mopac Output file
p -- PDB file
shelx -- ShelX file
spar -- Spartan file
mol -- Sybyl Mol file
mol2 -- Sybyl Mol2 file
x -- XYZ file
The -o flag is used to set the output file type. The following output
type codes are currently supported.
Currently supported output types
diag -- DIAGNOTICS file
t -- Alchemy file
bs -- Ball and Stick file
caccrt -- Cacao Cartesian file
cache -- CAChe MolStruct file
c3d1 -- Chem3D Cartesian 1 file
c3d2 -- Chem3D Cartesian 2 file
d -- ChemDraw Conn. Table file
cssr -- CSD CSSR file
diag -- DIAGNOTICS file
gamin -- Gamess Input file
gcart -- Gaussian Cartesian file
g -- Gaussian Z-matrix file
hin -- Hyperchem HIN 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
p -- PDB file
report -- Report file
spar -- Spartan file
mol -- Sybyl Mol file
mol2 -- Sybyl Mol2 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 -ix myfile.xyz -renum -oai 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 -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.
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 "1-5" -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.
GAUSSIAN FILES
Babel 1.1 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 -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
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.
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
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
Babel 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
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