[gmx-developers] ffcharmm in gromacs-4.0 patches

Joshua Adelman jadelman at berkeley.edu
Sat Apr 11 08:34:46 CEST 2009

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  

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  

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.


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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