AMBER: coordinate changes using ptraj

From: Mike Summers <>
Date: Sat, 3 Mar 2007 19:34:24 -0500

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.


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
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Received on Sun Mar 04 2007 - 06:08:13 PST
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