I don't think you should minimize in vacuum. That will likely change the
structure
too much. Maybe if you can tell us what your goals are we can tell you how
to
get a structure for it- perhaps the average structure would be best, perhaps
the
representative structure from cluster analysis, etc.
On 3/3/07, Mike Summers <summers.hhmi.umbc.edu> 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: summers.hhmi.umbc.edu
> Web: www.hhmi.umbc.edu
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Received on Sun Mar 04 2007 - 06:08:13 PST
