[gmx-developers] ffcharmm in gromacs-4.0 patches

Justin A. Lemkul jalemkul at vt.edu
Sat Apr 11 13:51:14 CEST 2009

Joshua Adelman wrote:
> I'm attempting to use the ffcharmm force-field found in the cvs version 
> of gromacs (patches update). I'm having some problems with pdb2gmx, that 
> I was hoping someone could give me a hand with. I'm a little new to 
> working with gromacs, so I may be making a really silly beginner's 
> mistake, but when I run pdb2gmx on my system using the -ff charmm27 flag 
> (pdb generated by vmd from a namd simulation), I'm getting a bunch of 
> errors related to the histidine residues, of the form:
> WARNING: atom HN is missing in residue HSD 64 in the pdb file
>          You might need to add atom HN to the hydrogen database of 
> residue HSD
>          in the file ff???.hdb (see the manual)
> The ffcharmm27.hdb does not contain an entry for histidines named HSD, 
> but does use what looks like the standard gromacs HISA, HISB, etc. 
> However if you look in the .rtp file, there is an entry for HSD, HSE but 
> nothing for HISA,HISA, etc. When I look in other forcefields in the /top 
> directory, it seems like other force fields are consistent in their 
> naming schemes between these file types (for example in ffoplsaa.*)
> I've tried renaming my histidine residues to HIS, using the interactive 
> -his flag, etc, and I just get different conflicts that seem to be 
> related to this inconsistency between the files that I mention above.
> Is this a problem with the ffcharmm files, or am I just doing something 
> wrong?

Try creating entries in the .hdb file (HSD = HISA, HSE = HISB) and see if that 
fixes it.  If it works, then the .hdb file available in CVS may have to be updated.


> Any suggestions would be most appreciated.
> Josh
> ------------------------------------------------------------------------------------------------------ 
> Joshua L. Adelman
> Biophysics Graduate Group              Lab: 510.643.2159
> 218 Wellman Hall                                Fax: 510.642.7428
> University of California, Berkeley     http://nature.berkeley.edu/~jadelman
> Berkeley, CA 94720 USA                   jadelman at berkeley.edu
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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