AMBER Archive (2008)

Subject: Re: AMBER: ptraj - closest command

From: Jianyin Shao (jyshao2004_at_gmail.com)
Date: Wed Oct 08 2008 - 14:50:29 CDT

On Wed, Oct 8, 2008 at 11:36 AM, Ryan Pavlovicz <pavlovicz.7_at_osu.edu> 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_at_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_at_SG oxygen
> image :WAT byres
> rms first mass :13-146_at_CA,C,N:176-309_at_CA,C,N
> trajout in_trajout.crd
>
> go
> EOF
>
> 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.
Best,

Jianyin

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu