On Wed, Nov 13, 2013 at 7:10 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Many thanks Jason for the quick reply.
>
> In answer to your question, I applied the restrains to the whole complex
> (all protein residues, water, ligand).
>
> Looking at advanced tutorial 3 (
> http://ambermd.org/tutorials/advanced/tutorial3/section1.htm), the
> authors applied restraint_wt = 2.0. Isn't this excessive? Is there a reason
> for applying such restraint?
>
2 kcal/mol/A^2 isn't what I would call excessive. 100 kcal/mol/A^2 and
greater is what I would call excessive. 10 kcal/mol/A^2 are very strong
restraints, but not uncommon in my experience.
My last question is whether there is a way to tell whether my observation
> is an imaging artifact or not?
>
You need to image the whole system (e.g., with the 'autoimage' command in
cpptraj). 'Conserved waters' can still typically exchange with the bulk
solvent (and still be conserved). How do you know this is not happening,
or that it's a "bad thing" if it is?
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Nov 14 2013 - 04:30:03 PST
