[gmx-developers] CHARMM FF

Justin A. Lemkul jalemkul at vt.edu
Sat Jan 17 05:50:03 CET 2009

Mark Abraham 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.

I created one some time ago, and did a bit of testing with it.  I had no 
problems with proteins and simple test peptides, but that doesn't mean it's 
perfect.  Hopefully the attachment will come through; if not I can send it off-list.


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

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