2010/4/13 pxq <pangxueqintea.yahoo.com.cn>:
> Hello everyone,
>
> After running MDĦĦI want to pick out some water molecuar within a certain distance of a given molecular.
>
> There is a watershell option in ptraj that can count the number of waters within a certain distance of the given molecular. But it cannot tell which exact waters are they. so do you know any options or ways to get those waters for a .mdcrd file.
See the "closest" command and/or "closestwater" in ptraj. This sounds
like it does what you're looking for. It's described in the manual.
Good luck,
Jason
>
> Thanks so much for your kind help
>
> Best wishes
>
> Xueqin
>
>
> =============================================================================================================
> Pang Xueqin
> State Key Laboratory of Molecular Reaction Dynamics
> Dalian Institute of Chemical Physics
> Chinese Academy of Sciences.
> Tel: 0411-84379352 Fax: 0411-84675584
> ==============================================================================================================
>
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--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Apr 13 2010 - 05:30:02 PDT
