Dear gromacs users, I have one protein with phosphoserine and phosphothreonine. I want to do simulation, but I do not know which force field I have to use. None of the force field from gromacs has the information of phospho residues. Then I tried with charm36, but did work. Kindly suggest me what I can do.
Well, CHARMM36 has everything you need included, so unless you explain what "didnot work" means (because it's the single most useless phrase in debugging anything), there's little anyone can do to help you. Please describe exactly what the problem was (commands, output, errors, etc). -Justin Dear Justin, I solved the problem. That is only the mismatching of residue names and I renamed the residues in my PDB file. Now the problem is with OXT atom at C-terminal end.I other words the exact error is "Atom OXT in residue GLN 68 was not found in rtp entry GLN with 17 atoms while sorting the atoms ". I understood the error. rtp file does not have the atom OXT information. How could one solve this problem? Thanks in advance Surya Graduate student India. -- 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.