[gmx-users] atomtype problem (was Re: gmx-users Digest, Vol 77, Issue 138)

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 22 22:32:30 CEST 2010

I've gone ahead and changed the subject line to potentially attract the 
attention of others who might help.

lloyd riggs wrote:
> Dear All,
> I'm not sure if this is a bug or not.  I downloaded and installed the new
> version of Gromacs, and compiled it fine, and recompiled just mdrun_mpi....
> The problem I now encounter.  U was using 53a6 FF, which worked in the past,
> although I am partial to all atoms.  In Pro residues, the topolog output from
> grompp lables three of the CH2 in the ring as CH2r.  When I then do an EM or
> MD, gromacs complains that it can not find atom type CH2r.  I looked through
> all the .itp, .rtp and amino acid definitions, and CH2r is there.  If I
> re-lable the topology and .gro file by hand to CHR1 the system works, but the
> overall geometry is slightly off (if you look at the atom definitions and
> take into account that prolines are not completly aeromatic, only
> partially...

Well, proline isn't aromatic at all, but CHR1 will try to force the atoms to be 
planar.  None of this should be necessary (nor is it right to do).

> In any case, is this a bug or is there some other problem I missed?  I did
> look at the input .pdb file, and the same nomenclature I used before with the
> same ff now does not work?

All signs point to the fact that processing of proline should work out of the 
box, so to speak.  The CH2r atom type is properly defined in all the relevant 
files.  Can you post a bit more detail, like the exact error message, snippet 
from the topology, etc?  I haven't had any problem with proline-containing 
proteins with 53a6 in the newest version.


> Sincerely
> Stephan Watkins


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list