Dear GROMACS experts: I'd tried to use a GBSA implicit solvent function in ver. 4.5.4. I'd convinced the normal run with vacuo with simply high epsilon_r setting. After that, I'd modified the topology stuff by adding "[ implicit_genborn_params ]" entry and then implicit_solvent = GBSA gb_algorithm = OBC gb_epsilon_solvent = 78.3 in the mdp file to try a GBSA implicit solvent run.
Then I'd suffer error from grompp like as "Fatal error: Cannot find length for atoms 1-3 involved in angle". Actually, there is no covalent bond between 1-3 (there is an angle with atoms 1-2-3, but these are bonded only with 1-2 and 2-3). I'm wondering what kinds of extra-modification in topology stuff besides adding "[ implicit_genborn_params ]" entry for the implicit solvent runs from the runs without it. Any info. will be welcome. Thank you for advance. Makoto Yoneya, Dr. AIST, Tsukuba JAPAN http://staff.aist.go.jp/makoto-yoneya/ -- 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
