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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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