Re: [AMBER] Translate command with ptraj

From: Thomas Cheatham III <>
Date: Sat, 11 Dec 2010 17:19:14 -0700 (Mountain Standard Time)

> I have investigated this issue with several test cases with both ptraj and
> VMD (and checked the ptraj source code in action.c). Simply translating does
> not take into account the gamma=120 angle of my unit cell, i.e. translation
> does not reproduce the periodic images from my simulation. As a result, I am
> not obtaining the correct interfaces in my filtered trajectory. Does anyone
> know of a way to translate along unit cell dimensions that are not all
> orthogonal to one another?

As you observe, the translate command has no concept of the periodic unit
cell... Moreover, unless the periodic box was fixed (constant volume) and
the molecules fairly rigid you would have a difficult time predicting for
each frame what distance should be translated to preserve the interface...

I think what you want is not "translation" but imaging, and instead of
imaging to the unit cell, imaging to nearby unit cells. This can be done
using the xoffset/yoffset/zoffset values to the image command. I also see
that I neglected to add this to the manual (d'oh!).

If you want to image your molecule, say residues 1-100 to the unit cell in
the +x direction,

image :1-100 xoffset 1.0

To, for example, build up a whole series of unit cells around my original
cell I run ptraj multiple times with all combos +/- 1.0, 0.0 to get this.
See a csh script below.



#!/bin/csh -f

set rst = $1

foreach x (0 1 2)
  foreach y ( 0 1 2)
     foreach z ( 0 1 2 )

ptraj prmtop <<EOF

trajin $rst
trajout img_$x$y$z.pdb pdb
strip :WAT
center :1-24
image xoffset $x yoffset $y zoffset $z


mv img_$x$y$z.pdb.1 img_$x$y$z.pdb

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Received on Sat Dec 11 2010 - 16:30:03 PST
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