Hi, These errors mean exactly what they say. There's a mismatch between your structure file and the residue structure in the database. So you need to look at them both and see what is wrong. Chapter 5 of the manual is your friend.
Mark On 19/03/2015 3:17 am, "RJ" <ra...@kaist.ac.kr> wrote: > Dear gmx, > > > I tried to to use pdb2gmx and get this error for 3 to 4 residues. I even > cleaned my crystal structure using Discovery studio/swissviewer which shows > no error on it. I wonder, how do i rectify this problem ? > > > WARNING: WARNING: Residue 1 named MET 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 366 named LEU 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: 7060 pairs > > > Residue 32681 named GLN of a molecule in the input file was mapped > to an entry in the topology database, but the atom N used in > an interaction of type improper in that entry is not found in the > input file. Perhaps your atom and/or residue naming needs to be > fixed. > -- > 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.