Re: [AMBER] Ptraj problems

From: Thomas Cheatham <>
Date: Mon, 14 Jun 2010 03:46:47 -0600 (Mountain Daylight Time)

> We have had much problems with wrapping with ptraj.
> Here is an example, where we try to centre on the first atom and wrap
> into an octahedral box, but we get a number of waters at a distance and
> therefore also a wrong centering.

I believe you want to center about residue #1 and then image. Your script

trajin m1
trajout pdb pdb
image origin center familiar com :1

What you want is:

trajin m1
trajout pdb pdb
center :1 mass origin
image origin center familiar


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Received on Mon Jun 14 2010 - 03:00:04 PDT
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