Many thanks Dan,
much appreciated
George
On Jan 12, 2012, at 7:21 PM, Daniel Roe wrote:
> 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 - 11:00:02 PST
