AMBER Archive (2007)

Subject: AMBER: coordinate changes using ptraj

From: Mike Summers (summers_at_hhmi.umbc.edu)
Date: Sat Mar 03 2007 - 18:34:24 CST


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_at_hhmi.umbc.edu Web: www.hhmi.umbc.edu ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu