Hi, According to the output for "gmx help pdb2gmx",
"Default termini are ionized (NH3+ and COO-), respectively. ... The AMBER force fields have unique forms for the terminal residues, and these are incompatible with the -ter mechanism. You need to prefix your N- or C-terminal residue names with "N" or "C" respectively" I'm using AMBER99SB. So, for example, I have to change the residue name for my N-terminal leucine from LEU to NLEU. Is it right? I'm in doubt because this would make my pdb non-standard. Indeed, the visualization becomes messy in PyMOL after this change. Moreover, I need to use the noter option for pdb2gmx, am I right? -- 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.