Hi,
On Thu, Jan 12, 2012 at 12:29 PM, George Tzotzos <gtzotzos.me.com> wrote:
> I've checked the AmberTools manual for the ptraj action command "closest".
>
> My question is whether there is a distance cutoff between the residues specified in the mask and the first atom in the solvent molecule.
The 'closest' command doesn't use any cutoff, it modifies the
coordinate frame to include the closest # of specified waters no
matter how far away they are.
> A related question is whether there is a way to work out the -per frame - number of solvent molecules buried in the binding site of a receptor/ligand complex in the course of trajectory.
I don't think so, not directly at least. You *might* be able to glean
similar information using the watershell command with an appropriate
mask and distance cutoffs, but you'd have to be careful not to
over-interpret the results.
-Dan
>
> Thanks in advance for any advice
>
> Regards
>
> George
>
>
>
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--
-------------------------
Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ 08854
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Received on Thu Jan 12 2012 - 10:30:03 PST
