Hi, I suggest you produce your initial conformation in .gro format, which permits five-character atom names. That might mean using editconf on your .pdb file, and then manually renaming atoms.
Mark On Fri, Jun 23, 2017 at 3:55 AM Qing Lv <lvqingjie...@163.com> wrote: > Hi, > > > Gromos 54a7 force field has built-in topologies for some small molecules, > like ATP. In these topologies, many atoms have names of up to 5 letters, > such as AO1PA and AO2PB. However, PDB files seem do not support 5-letter > atom names. So, if I name an atom "AO2PB" in PDB, it will be truncated to > "AO2P" or "O2PB" when executing pdb2gmx, and these atoms cannot be > recognized then. > Anyone know how to solvate this problem? Many thanks ^_^ > > > Qing > -- > 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.
