On Wed, May 11, 2016 at 8:16 AM, Indrajit Deb <biky2004indra.gmail.com> wrote:
> The following cpptraj output is showing that it considering the geometric
> center between the selected atoms in the mask, but I want to consider the
> oxygen atom of the water molecule to calculate the distance from the
> geometric center. For that, I used the 'oxygen' key. But the output showing
> that only first atom of the solvent molecule was used for distance
> calculation.
The first atom in a water molecule for most explicit water models
(TIPXP, SPC, etc) is the oxygen. You can verify this yourself via
something like:
cpptraj -p <topology> --mask ':WAT' | head
So I think things are OK. Is your output trajectory not what you
expected? Maybe I'm just not understanding your question. Let me know
if this doesn't clear things up.
-Dan
>
>
> CLOSEST: Finding closest 1 solvent molecules to atoms in mask :5.HN1,O2P
> Geometric center of atoms in mask will be used.
> Only first atom of solvent molecule used for distance calc.
>
>
>
> Please explain what wrong I am doing.
>
> Best,
> indrajit
>
>
>
> --------------------------------------------------------------------------------------------------------------
> *Indrajit Deb*
> alternate emails: indrajitdeb81.gmail.com, idbmbg_s.caluniv.ac.in
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> ).
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
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Received on Wed May 11 2016 - 08:30:03 PDT
