Hi all:
I was working with a protein-ligand complex using CNS, way back when,
and have moved my calculations over to Xplor-NIH, in part to make use
of its facilities for multiple conformer interpretation of NOEs and
other refinement goodies.
I generated my ligand parameters using Xplo2D. When implemented in
CNS I had no problems with the ligand's naphthalene ring deviating
from planarity. After scrutinizing the parameter file (and consulting
with Xplo2D's author, Gerard Kleywegt) I am quite certain the
planarity ought to be maintained in Xplor-NIH. Nonetheless, the
naphthalene ring is puckering in my current calculations.
I can get these problems with the example script gb1-anneal.py using
version 2.16.4 on an Intel-Mac. I initialize the protein and ligand
topologies and parameters as follows:
=======================================
from psfGen import seqToPSF
seqToPSF( "protein.seq", startResid=1 ) #defines topology; invokes
protein parameter set?
import protocol
protocol.initCoords( "protein-coordinates.pdb" ) #initial coordinates
for protein
protocol.addUnknownAtoms()
command = xplor.command
command("parameter @ligand.par end") #defining ligand parameters...
command("structure @ligand.psf end") #...topology...#
command("coordinates @ligand.pdb end") #...coordinates#
=======================================
I have tried increasing the scaling terms for the improper angles, to
no avail.
I thought this might be an artifact of torsion mode dynamics but the
problem persists through cartesian-only dynamics.
So I think this has something to do with how I'm initializing this
with Xplor-NIH.
Thanks in advance for any assistance,
Ryan
Ryan M.B. Hoffman,
PhD. Candidate.
Department of Biochemistry,
University of Alberta
Phone: (780) 492-3006
http://www.bionmr.ualberta.ca/rydog/
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20070507/ea1fbffa/attachment.html
