I have a general procedural question. I have used amber
to generate RNA NMR structures using Na+ and explicit water.
As I understand it, final minimization should probably be
done without the water. I therefore would like to
use ptraj to strip out the water after doing the MD
calculations and save the restart file that does not
have water. I would then use the water-less restart file
for final minimizations in vacuo.
The potential problem is that, if the coordinates are
modified by the strip command, I think this will lead to major
RDC violations. Is it possible to strip the water and Na+ atoms
without changing the coordinates? Or can I use
a reference structure to reset the coordinates after
I strip the water out?
I'm having what I think is a related problem in a calculation
I'm doing now, in which I use a reference structure to hold
atoms rigid during an MD (in water, Na+) simulation. After
doing the MD, if I use ptraj to strip the water and save a
water-less restart file, the restart file LOOKS good when I
view it in pymol, but when I use it to start a restrained
minimization (again, using a reference structure to fix
some of the atoms), the amber energies are off the charts...
I think because of major changes that are made to try to satisfy
the restraints to the reference structure.
Thanks for any suggestions.
Mike
--
*********************************
Michael F. Summers
Department of Chemistry and Biochemistry
and Howard Hughes Medical Institute
University of Maryland Baltimore County
1000 Hilltop Circle
Baltimore, MD 21250
Phone: (410)-455-2527
FAX: (410)-455-1174
Email: summers.hhmi.umbc.edu
Web: www.hhmi.umbc.edu
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Received on Sun Mar 04 2007 - 06:08:13 PST
