Dear GMX user, As you know, naming the Hydrogen atom differently in different FF and in .pdb or .gro file brings lots of problems in the "gmx pdb2gmx". I also met the issue when I wanted to convert my self-made (by Avogadro) heptapeptide.pdb to heptapeptide.gro file.
I could get rid of them using "-ignh" which is ignoring H atom in the heptapeptide.pdb file.Then, If I understood correctly this means no normal Hydrogen atom there is in produced heptapeptide.gro file?! If so, do you think if this makes sense proceed further with a peptide which is missing the normal hydrogen atom in? Thanks. Cheers, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
