Hi, As suggested above, use -ignh to ignore hydrogen atoms. To use a specific Histidine, you may change residue name HIS to HIP(Amber)/HSP(Charmm)/HISH( OPLS ) or HID(Amber)/HSD(Charmm)/HISD( OPLS ) or HIE(Amber)/HSE(Charmm)/HISE( OPLS ) either in PDB file or interactively through pdb2gmx usng -his command.
On Wed, Mar 30, 2016 at 12:27 PM, bio hpc <biohpc2...@gmail.com> wrote: > Hi, > > we have created some protein pdb files with Maestro. When we try to un an > MD simulation with gromacs, we get errors like: > > >> Atom HD11 in residue ASN 5 was not found in rtp entry ASN with 14 atoms > > I tried to find a solution and it seems that internal gromacs dictionary > for hydrogens is different from the one from Maestro and other formats. It > seems, from what I read, that one must convert all hydrogen types to > Gromacs format. Is is there any script that can do this automatically? > > Of course, there is the option “ignore hydrogens”, but this would be bad > for us, since we need some histidines in the binding site, and so on. > > Thanks, > BIO-HPC > > > > -- > 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.