[gmx-developers] CHARMM FF

Roland Schulz roland at utk.edu
Sat Jan 17 06:03:17 CET 2009


in 4.0.3 (from cvs) charmm is included. Sorry for not mentioning the
version. Generating the hydrogens works. What does not work, is using
existing hydrogens.


On Fri, Jan 16, 2009 at 10:18 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> Roland Schulz wrote:
>> Hi,
>> there seems to be something wrong with the sorting and identification of
>> hydrogens in pdb2gmx when using CHARMM FF.
>> It does not identify the hydrogen atoms correctly if they are already
>> present, even if the names all match.
>> To reproduce: Generate pdb with hydrogens using pdb2gmx. Then use this pdb
>> as input of pdb2gmx again.
>> Result e.g.:
>> Atom H in residue VAL 2 not found in rtp entry with 16 atoms
>> This does not happen with GROMOS or OPLS FF.
> Sure. AFAIK nobody has written a functional ffcharmm.hdb file, so
> generation will not work. If someone has a need for one, they can write one.
> I'll be happy to include it in my GROMACS-CHARMM package.
> Mark
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ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
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