Dear Mark,
Actually I had tried the method you suggested, but got such errors (pdb2gmx): Fatal error: Atom O1 in residue ILE 294 was not found in rtp entry ILE with 9 atoms while sorting atoms. ILE294 is C-terminus of my protein. I looked up in aminoacids.rtp and there are no atom "O1" or "O2" in ILE entry; however, I never got such errors when using pdb2gmx to process PDB files. Maybe, pdb2gmx can only process terminal residues for PDB files? Also, I have tried to process protein and ATP separately with pdb2gmx and then combined them together, but met problems. That's why I sent another 2 emails... Qing At 2017-06-23 15:33:17, "Mark Abraham" <mark.j.abra...@gmail.com> wrote: >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. -- 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.