Re: [AMBER] how to pick certain water molecular from a .mdcrd

From: Thomas Cheatham <>
Date: Tue, 13 Apr 2010 21:00:27 -0600 (Mountain Daylight Time)

> After running MD I 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.

The command you want is "closest"

closest 5 :1

will save the closest 5 waters to residue 1. Note that the numerical
identity of the waters will not be preserved so you can not look at
commands like "diffusion" on this adapted trajectory. Also, you will need
a prmtop with with 5 waters to process/watch movies/analyze further.


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Received on Tue Apr 13 2010 - 20:30:02 PDT
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