VMD-L Mailing List

From: ѩ Pang Xueqin (pxq_at_dicp.ac.cn)
Date: Tue Apr 13 2010 - 01:37:16 CDT

Hello everyone,

      After running MDI want to pick out some water molecuar within a certain distance of a given molecular.

      There is a watershell option in ptraj(amber package) 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.

Thanks so much for your kind help

Best wishes

Xueqin


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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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