[gmx-users] residue names for AMBER ff in GROMACS
Justin A. Lemkul
jalemkul at vt.edu
Sun Mar 30 17:13:00 CEST 2008
Quoting OZGE ENGIN <OZENGIN at KU.EDU.TR>:
> 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
> So, what may be the problem?
> Thanks in advance
> Ozge Engin
> Computational Science & Engineering
> Koc University
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul at vt.edu | (540) 231-9080
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