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

[Justin A. Lemkul]

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:

http://chemistry.csulb.edu/ffamber/#usage

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

-Justin

>
> 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
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================