On Wednesday, August 12, 2009 at 8:47:33 PM, Nancy <nancy5vi...@gmail.com> wrote:
> In an earlier message, it was stated that topolbuild generated topologies with Gromos 53a6 > and OPLS-AA force fields. I am using topolbuild (version 1.2.2), and the only files in the > "dat/gromacs" directory are for the force fields: 43a1, 43a2, 43b1, 45a3, 53a5, and 53a6. > How is the OPLS-AA force field used? First, I need to thank you in particular. First, while testing your molecules, I discovered a case in the as yet unreleased topolbuild 1.3 in which my dihedral selection method failed to select the dihedral choice with the maximum number of heavy atoms with OPLS-AA as the force field. Second, also because of this, I discovered what one downloads as a "Sybyl 2" structure from one source of small molecule structures and how to edit it so that it meets the syntax standards for a true mol2 file. Thank you very much for this assistance. In the earlier message, I stated that topolbuild 1.2.1 ( and 1.2.2) generates topologies for amber, gaff, glycam, 43a1, 43a2, 43b1, 45a3, 53a5, and 53a6. I stated that the as yet unreleased topolbuild 1.3 will include OPLS-AA. The version of topolbuild you have, is 1.2.2. Would you like to beta test topolbuild 1.3? Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273
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