CCL Home Page
Up Directory CCL README.1ST
	      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.
--------------------------------------------------------------------------

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













Modified: Tue Feb 28 17:00:00 1995 GMT
Page accessed 7447 times since Sat Apr 17 22:03:24 1999 GMT