Sorry, maybe it's [molecules]. Chapter 5 is your best friend ;-) Mark
On Wed, Jan 6, 2016 at 9:35 PM Irem Altan <irem.al...@duke.edu> wrote: > Hi, > > I have a .pdb file that I generated by creating three more copies of the > protein according to its P212121 symmetry. I am now trying to run pdb2gmx > on it, but I get the following error: > > Fatal error: > Residue 111 named CYS of a molecule in the input file was mapped > to an entry in the topology database, but the atom CA used in > that entry is not found in the input file. Perhaps your atom > and/or residue naming needs to be fixed. > > What is weird is that there is no residue 111 that is a cysteine (residue > 111 is a phenylalanine). I had run MD simulations successfully on a single > copy of this protein before. pdb2gmx runs without an error when I use the > old .pdb file. What could be the problem? > > Best, > Irem > -- > 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. > -- 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.