I got frustrated with the options for building topologies for ligands and wrote this to allow me to use bond length and angle values derived from prior modeling and NMR data. There probably will be something better than this from the developers at some point, but I decided to upload what I have to Gromacs contributed software.
To build a gaff or amber## based topology, the builder requires the antechamber atom type definition files and the gaff and amber## parm files as found in the dat directory for antechamber-1.27 (files in directories dat/antechamber and dat/leap/parm). To build a Tripos force field based topology, the builder requires the TAFF* files found in the Tripos directory pointed to by the Tripos variable $TA_ASCTABLES . The builder has options to renumber atoms and residues to decrease the editing required to add a ligand to a system, to revise atom naming for consistency (only useful with small molecule ligands), and to use bond lengths and angle values derived from coordinates instead of set by the force field. The builder also converts Tripos distance restraints to Gromacs distance restraints. (As noted in the NOT_DONE file in the submission, there seem to be some differences between what Tripos gives as an angle restraint and what Gromacs wants as an angle restraint.) The file is topolbuild.tgz and includes a text file describing the testing I've done so far of topologies built with this program (PROGRAM_TESTING_DONE) along with other descriptive material including indications of possibilities for expansion to other all atom force fields. As noted above, the NOT_DONE file indicates things this contribution does not include. INVENTORY is a list of all files in the contribution. PROGRAM_UNITS lists the program files in the contribution and the purposes they serves, and lists seperately the header files and the program files that call for them. The README should be enough for installation and usage documentation. Note that the antechamber and Tripos force field files are not included in the contribution. These will have to be placed in appropriate directories separately. This contribution does, however, include water and ions force field files suitable for use with gaff. I hope this proves useful to somebody. Sincerely, Bruce D. Ray, Ph.D. Associate Scientist, and Operations Director NMR Center IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 USA ____________________________________________________________________________________ Park yourself in front of a world of choices in alternative vehicles. Visit the Yahoo! Auto Green Center. http://autos.yahoo.com/green_center/ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php