Re: AMBER: coordinate changes using ptraj

From: Carlos Simmerling <>
Date: Sat, 3 Mar 2007 19:44:00 -0500

I don't think you should minimize in vacuum. That will likely change the
too much. Maybe if you can tell us what your goals are we can tell you how
get a structure for it- perhaps the average structure would be best, perhaps
representative structure from cluster analysis, etc.

On 3/3/07, Mike Summers <> wrote:
> 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:
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Received on Sun Mar 04 2007 - 06:08:13 PST
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