Mike- I'm a bit confused. Is your system an ligand/enzyme with active site
or RNA with
explicit counterions? maybe it's both, just checking since your different
posts
seem to imply a different system. For gas phase min RNA/DNA would
not be good due to the charges. Perhaps for a protein it may be ok. You
would
probably want to at least include a continuum solvent like GB during min.
Also in your first mail you said you were worried about RDC violations-
do you have RDC data?
The problem with annealing is as you suggest- there is no "perfect"
annealing
protocol. All you can really do is try a few times using different protocols
and
see if the final results are consistent. If they differ, it means your
results depend
on the protocol and therefore may not be ideal.
As fas as the high energies after restarting, I'm still not exactly clear on
what's going on. Are you restarting with water/ions, or no?
On 3/3/07, Mike Summers <summers.hhmi.umbc.edu> wrote:
>
> 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.
>
> Mike
>
>
>
> 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 <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
> > >-----------------------------------------------------------------------
> > >The AMBER Mail Reflector
> > >To post, send mail to amber.scripps.edu
> > >To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> > >
>
> --
>
>
> *********************************
> 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
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
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Received on Wed Mar 07 2007 - 06:07:07 PST
