On 12/14/12 3:20 PM, James Starlight wrote:
Justin,
in the case of the system with the atom types assigned from that paper
the grompp produced above 118 errors of non standard bond, angle as
well as dihedral types ;o So it' seems that some 118 addition terms
must be added to the ffbonded.itp to the existing charmm parameters(
it's uncommon for me because in that case the atom names werefrom
standart charmm ff but the total number of errors was bigger than in
case of Swiss params non-standart names usage).
I'm not sure why there were so many errors when you used those parameters. Like
I said, we've used them before. I recall a few errors along the way, but manual
assignment of the bonded parameters according to the paper is fairly
straightforward.
By the way I've simulated choromophore produced by SWISS ( with the
charges assigned from the paper) in the vacuum and didnt notice any
inaccuracy in the conformation of chromophore. So the last that I
should is the carefull assignment of the 9 missed dihedral terms with
the rest of the protein.
Sounds like a reasonably approach. Good luck.
-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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