Hi You have to update your rtp and hydrogen atom files in respective ff.
On Thu, 14 Dec 2017 at 1:13 PM, Vishwambhar Bhandare <vishway...@gmail.com> wrote: > Hi, > I get this error while running pdb2gmx, > > > > *"Atom HG1 not found in rtp database in residue PRO, it looks a bit like > HG2"* > the proline is modified,,,In my structure, > 'HG1' is replace with 'F'. > The N-terminal and C-terminal are capped with ACE and NH2 respectively... > I tried with OPLS and AMBER ILDN force field.. > > I modified proline atom in force field file as given below, > > [ PRO ] > [ atoms ] > N N -0.25480 1 > CD CT 0.01920 2 > HD1 H1 0.03910 3 > HD2 H1 0.03910 4 > CG CT 0.01890 5 > F HC 0.02130 6 > HG2 HC 0.02130 7 > CB CT -0.00700 8 > HB1 HC 0.02530 9 > HB2 HC 0.02530 10 > CA CT -0.02660 11 > HA H1 0.06410 12 > C C 0.58960 13 > O O -0.57480 14 > [ bonds ] > N CD > N CA > CD HD1 > CD HD2 > CD CG > CG F > CG HG2 > CG CB > CB HB1 > CB HB2 > CB CA > CA HA > CA C > C O > -C N > [ impropers ] > CA +N C O > -C CD N CA > > > How this issue can be resolved?? > > Thanks in advance > > > -- > Vishwamhbar Bhandare > Research Associate > Bose Institute, > Kolkata-54 > -- > 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. -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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.
