I am trying to figure out changes made in v 4.5.1 in share/gromacs/top. In earlier versions, there were some defined variables, e.g., hyp_prop_1 for hydroxyprolines and
grep -r hyp_prop_1 ~/gromacs_4.0.5/share/gromacs/ top/ would show ~15 lines, including for example: ffamber99bon.itp:#define hyp_prop_1 0.65270 1.95811 12.46832 -2.61082 0.00000 0.00000 ; HYP for amber99: S Park, R J Radmer, T E Klein & V S Pande (submitted). If I grep the version 4.5.1 directories, nothing is found. Grepping either for hyp or for 1.95811 (one of the values above) does not find anything either. Seaarching for one of the author names from the above output finds entries in aminoacids.rtp files, but there are no dihedral parameters for Hyp listed there. Where are the Hyp torsion parameters ?
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
