[gmx-developers] ffcharmm in gromacs-4.0 patches

Erik Lindahl lindahl at cbr.su.se
Sun Apr 12 19:41:12 CEST 2009

Hi Joshua,

Please send this PDB file to bjelkmar at cbr.su.se (and say that I told  
you to ;-) - we're working on the final termini patches as well as the  
histidine detection - including hydrogen-bond-based protonation state  
selection (I think there could be some hardcoded name changes  



On Apr 11, 2009, at 8:34 AM, 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?
> 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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