[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

Justin Lemkul jalemkul at vt.edu
Tue Dec 11 23:06:24 CET 2012

On 12/11/12 4:13 PM, James Starlight wrote:
> Today I've made parametrization of the chromophore group by means of
> Swiss param and integrated that topology into charmm27 ff. The only
> problem that I have is with the N-term N atom of the chromophore. It's
> likely that I made mistake to parametrize it into full protonated form
> (NH2).

Protonation states of termini can indeed cause problems.  Model compounds often 
use capping groups (methyl, acetyl, etc) to mitigate these effects.  You can 
probably get some tips from http://pubs.acs.org/doi/abs/10.1021/jp014476w, or 
otherwise just use their parameters.

> When I've used pdb2gmx on the GFP structure the peptide bond between
> that N atom and adjacent O ( from C term of adjacent residue) is
> incorrect ( both oxygens preserves on the C atom so my system had
> divided onto 2 chains as well as had incorrect charge). How I could
> define the N atom in the topology as the N-terminal? (I've delited
> both hydrogens from RTP as well as from HDB files but the problem
> didn’t resolved. Also I'm using -ignh on the input pdb to ignore all
> hydrogens from the model)

Copying and pasting your .rtp and .hdb entries would help.  Also note that the 
chromophore needs to be defined as protein in residuetypes.dat, otherwise the 
protein chain will terminate erroneously and you'll get protonation state problems.



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


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