Dear all, I am setting up a system with GROMACS 4.5.3 and the CHARMM force field. In the protein, I have a neutral lysine, for which CHARMM force filed has a specific residue type (LSN). When I wrote LSN as residue name in the initial pdb file, the topology file was perfectly created by pdb2gmx. However, in the next step, grompp complained about the CMAP torsion between the two previous residues:
Fatal error: Unknown cmap torsion between atoms 2747 2749 2751 2754 2757 However, if the LYS residue was written in the initial pdb file and the -lys option included with pdb2gmx (chosen the neutral protonation state for this lysine), grompp did not complain. The problem is that there is a deprotonated tyrosine (bound to a metal) in my system. I created a new residue type, but again the grompp complained about the CMAP between the two previous residues. Unfortunately, in this case I can't fit the problem with any of the pdb2gms options. I think the problem arises when a non-standard residue is included in the initial pdb file. Does someone else find this problem? I would appreciate any advise about how to solve it. Thanks in advance Jon -- 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
