You need to add the particular H to the amino acid .rtp file in the forcefield folder
On Fri, Sep 14, 2018, 4:24 PM AKANXA TIWARI <akanxatiwar...@gmail.com> wrote: > i am getting a warning after converting pdb2gmx and then applying force > field what i will do. please help me.i get this on screen. > WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was > mapped > to an entry in the topology database, but the atom H used in > an interaction of type angle in that entry is not found in the > input file. Perhaps your atom and/or residue naming needs to be > fixed. > > > > WARNING: WARNING: Residue 374 named PHE of a molecule in the input file was > mapped > to an entry in the topology database, but the atom O used in > an interaction of type angle in that entry is not found in the > input file. Perhaps your atom and/or residue naming needs to be > fixed. > > > Before cleaning: 6050 pairs > Before cleaning: 7868 dihedrals > Making cmap torsions... > There are 2709 dihedrals, 1833 impropers, 5404 angles > 6050 pairs, 3705 bonds and 0 virtual sites > Total mass 40604.576 a.m.u. > Total charge 11.000 e > Writing topology > > Back Off! I just backed up posre.itp to ./#posre.itp.1# > > Writing coordinate file... > > Back Off! I just backed up actin_asp_processed.gro to > ./#actin_asp_processed.gro.1# > --------- PLEASE NOTE ------------ > You have successfully generated a topology from: actin_asp_clean.pdb. > The Gromos54a7 force field and the spce water model are used. > --------- ETON ESAELP ------------ > > GROMACS reminds you: "Miggida-Miggida-Miggida-Mac" (Kriss Kross) > > akanxa@akanxa-HP-Notebook:~/Documents/aasp$ > -- > 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.
