1. Antechamber, http://amber.scripps.edu/antechamber/antechamber.html
2. RESP, http://amber.scripps.edu/ftp/plep.tar.gz
3. OpenBabel, http://openbabel.sourceforge.net
4. Gamess, http://www.msg.ameslab.gov/GAMESS/GAMESS.html
5. Gromacs, http://www.gromacs.org

These scripts are released under the GNU General Public License. See LICENSE.txt for details. In particular note that this software comes with NO WARRANTY.

This software was created under Sarnoff's Bug-to-Drug® Engineered Identification and Countermeasures Program which is funded by the U.S. Army Medical Research and Materiel Command under Contract No. DAMD17-03-C-0082.

The people involved are:

• Charles Karney <ckarney@sarnoff.com>
• Vincent Finley
• Jason Ferrara <jeferrara@sarnoff.com>
• Qiang Wang

Questions, comments, and improvements on this work should be sent to ckarney@sarnoff.com

Here are the main objectives of these scripts:

• Allow Gamess to be used in conjunction with Antechamber for the assignment of partial charges by the RESP or AM1-BCC methods.
• Add hydrogens to a PDB file using Gromacs and adjust atom names and certain bond angles to conform to Amber's rules.

• The charges produced by the AM1-BCC method are symmetrized between chemically equivalent atoms (using respgen's symmetry detection).
• Antechamber produces several temporary files which mean that it is unsafe to run multiple instances within the same directory. This is addressed by placing the temporary files in a unique directory.

These scripts are written as filters expecting input on stdin and producing output on stdout. Diagnostic messages appear on stderr. Generally a -h option produces a description of the script. A -d option causes the temporary directory to be retained for diagnostic purposes. The auxiliary programs that these scripts call should be located in your PATH. These scripts were written and tested under Linux. They should work on other Unix platforms. (It is possible that we rely on GNU awk extensions. Let us know if this is the case.)

Here is a quick description of the scripts. More complete documentation is obtained by running the script with the -h option.

• gjftogcrt: Converts a general Gaussian input file (possibly in mixed Z-matrix and Cartesian form) into a pure Cartesian representation.
• gjftogms: Converts a Gaussian input file to a Gamess format. It does this by invoking gjftogcrt and using Antechamber to convert the result to a Z-matrix form. The Z-matrix input allows the use of delocalized coordinates during geometry optimization by Gamess. acreorder is used to reorder of the atoms in order that the Z-matrix makes sense.
• gmstoresp: Converts the log file produced with Gamess to an Antechamber file with RESP charges. The input file for Gamess can be created with gjftogms -r. OpenBabel is used to extract the coordinate information for the output file. RESP and Antechamber are used to calculate the charges and create the output file. (The starting point for this script was one written by Hans De Winter, Katholieke Universiteit Leuven, hans@s151h14.rega.kuleuven.ac.be, which is provided with the RESP distribution.)
• gmstobcc: Converts the log file produced with Gamess to an Antechamber file with AM1-BCC charges. The input file for Gamess can be created with gjftogms -a. OpenBabel is used to extract the coordinate information for the output file. A work-alike divcon output file is created and Antechamber is invoked requesting AM1-BCC charges. (This invokes divcon for which we use a dummy script.) Finally we invoke chargesym to symmetrize the charges.
• divcon: A dummy divcon program (which merely copies the previously prepared output file to divcon.out). The Makefile copies this to $AMBERHOME/exe.
• chargesym: This symmetrizes the charges in an Antechamber file using respgen to identify equivalent atoms.
• acreorder: Reorders the atoms in an Antechamber file following the bonds from a starting atom. This is sometimes necessary as a precursor to converting the molecule to a Z-matrix representation.
• addhydrogens: Adds the hydrogens to the protein in a PDB file. This invokes the Gromacs tool, pdb2gmx, to add hydrogens. The result is fixed up to comply with Amber conventions by g96topdb. gromacs.patch contains a patch to gromacs 3.2.1 to correct the angles in NH2 groups.
• g96topdb: Reads in a Gromacs96 (g96) file, performs OPLS to Amber atom type and residue translation, replaces hydrogen bond lengths with bond lengths consistent with Amber force field, corrects for the SH bond angle in CYS, and finally writes the result to a pdb file. Amber residue variants by including the variant code (ASH, CYX, GLH, HID, HIE, or LYN) in columns 73-75 of the output.
• gjfrenumber: Reads in a Gaussian input file and renumbers the atoms and converts numerical indexes in Z-matrix lines into symbolic indexes. This would allow two molecules in Z-matrix format to be bonded together with a straightforward edit of the files.
• antechamberfilt and babelfilt: These are simple scripts that change antechamber and babel into filters so that they can be used in pipes.