Re: AMBER: coordinate changes using ptraj

From: Mike Summers <>
Date: Sat, 3 Mar 2007 20:39:28 -0500

I probably misunderstood David's email. He indicated that I should probably
not cool the system to 0K with explicit solvent during simulated annealing.

I'm trying to generate a structure of a ligand docked to a crystal structure
using NOE restraints. I'm using the xray structure as a reference file to hold
all the atoms of the protein fixed, except for the active site. I generated the
ligand and crudely docked it to the xray structure with xleap, then added Na+,
water, and used the results as input for an MD run. I currently heat to
350 degrees, followed by cooling to zero degrees, and use the resulting
restart file as input for a final minimization run. Is this general approach
OK? Or, after the MD at 350 degrees, should I cool to some lower T (I don't know
what is best... 100 C?), then restart a minimization calculation?

I've seen different approaches describe on the web. Thanks for your help.


n Sat, Mar 03, 2007 at 07:44:00PM -0500, Carlos Simmerling wrote:
> 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 <> 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:
> >Web:
> >-----------------------------------------------------------------------
> >The AMBER Mail Reflector
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> >To unsubscribe, send "unsubscribe amber" to
> >

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
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Mar 04 2007 - 06:08:13 PST
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