AMBER: ptraj - closest command

From: Ryan Pavlovicz <>
Date: Wed, 8 Oct 2008 13:36:17 -0400

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:

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


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?

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Received on Fri Oct 10 2008 - 05:08:00 PDT
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