[gmx-users] residue names for AMBER ff in GROMACS

Justin A. Lemkul jalemkul at vt.edu
Sun Mar 30 17:13:00 CEST 2008


> Hi all,
> I had a problem of converting of definition of residue names of AMBER96 ff in
> GROMACS package.
> Although I changed the residue names acc. to those defined in AMBER96 ff in
> my PDB file, I had the following error: (I have searched the mailing
> archieves for this error.)
> WARNING: atom H is missing in residue GLN 1 in the pdb fileYou might need to
> add atom H to the hydrogen database of
> residue GLN in the file ff???.hdb (see the manual).

AMBER is very specific about its nomenclature.  I provided this link just a few
days ago to someone else who asked the same question:


Read the documentation from the ffamber ports carefully; there are several
caveats about usage that you should be aware of.


> I looked at both .rtp and hdb files in order to investigate whether there are
> missing residues in these files, but  the GLN residue name and the
> corresponding H names of this residue have been defined in .rtp and
> .hdb,respectively.
> So, what may be  the problem?
> Thanks in advance
> Ozge Engin
> =================================
> Computational Science & Engineering
> Koc University
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list