From: Joseph Bylund (
Date: Tue Apr 13 2010 - 05:30:48 CDT

Hi Xueqin,

I'm not entirely sure I understood the question. But I believe you can
select the waters of interest by using "water and within 5.0 of protein"
if for instance you were interested in a water shell within 5 angstroms
of the protein. It could easily be "within 5 of resname ATP" or
whatever else it is you're looking for. Then after exporting the
structure you just count the number of O's in HOH's (grep HOH|grep -c
?wateroxygen?). Hope that helps.


-------- Original Message --------
Subject: vmd-l: how to pick certain water molecular from a .mdcrd
From: ѩ Pang Xueqin <>
To: vmd-l <>
Date: 04/13/2010 02:37 AM

> 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
> =============================================================================================================
> Pang Xueqin
> State Key Laboratory of Molecular Reaction Dynamics
> Dalian Institute of Chemical Physics
> Chinese Academy of Sciences.
> Tel: 0411-84379352 Fax: 0411-84675584
> ==============================================================================================================