Hi, I would rename those atoms exactly as the .tdb file in your force field expects. And if that doesn't work, try deleting them and having pdb2gmx rebuild them.
Mark On Mon, Jan 1, 2018 at 5:53 AM Amir Zeb <zebami...@gmail.com> wrote: > Hi gmx users, > > Wishing you all a very happy new year 2k18. > > I have modified a particular Tyr residue to phosphorylated Tyr and renamed > as TP2 per forcefield recognizable name. I have used: > gmx pdb2gmx -f xxx.pdb -o xxx.gro -ignh -ter (as full command) > C36m ff > Gromacs v5.0.6 > NH3+ as N-terminus > COO- as C-terminus > TIP3P water model > > I am getting error: > > Fatal error: > Atom OXT in residue SER 287 was not found in rtp entry SER with 11 atoms > while sorting atoms. > > The C-terminus of my pdb file is pasted right here: > ATOM 4538 OC1 SER A 287 > ATOM 4539 OC2 SER A 287 > TER 4540 SER A 287 > END > > I am aware of that SER 287 is C-terminus residue but by which name should i > replace the terminal oxygen to cope with this error? > > Looking forward for your kind suggestions. > > Thanks in advance! > > ~Amir > -- > 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.
