Re: AMBER: ptraj - closest command

From: Jianyin Shao <>
Date: Wed, 8 Oct 2008 13:50:29 -0600

On Wed, Oct 8, 2008 at 11:36 AM, Ryan Pavlovicz <> wrote:

> Hi. I am trying to visualize an explicitly solvated MD trajectory to
> analyze waters in a protein active site. Since it is very difficult and
> CPU-intensive to visualize all of the waters in the entire system, i would
> like to strip all waters but for those that enter the binding pocket. It
> seems that the ptraj command 'closest' more or less should do what i want.
> I tried to keep the closest 50 waters to an atom of interest:
> closestwater 50 :15.SG oxygen
> Then i create a new prmtop file that has my protein in addition to 50
> waters, but the visualization in VMD seems incorrect. While all of the
> waters are surrounding the area of interest, many of the waters i am viewing
> seem to be intersecting each other or coming unreasonably close to the
> protein. Here is the entire script i am using:
> #!/bin/bash
> ptraj in.prmtop << EOF
> trajin in.crd
> closestwater 50 :15.SG oxygen
> image :WAT byres
> rms first mass :13-146.CA,C,N:176-309.CA,C,N
> trajout in_trajout.crd
> go
> Can any one spot a problem, suggest a fix, or suggest an alternate method
> to preserve the waters that enter the active site while stripping the
> others? Thanks.

I think you should do "image" command before the "closestwater" command.


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Received on Sun Oct 12 2008 - 05:07:09 PDT
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