Re: AMBER: Problem using Ptraj

From: Thomas Cheatham III <>
Date: Mon, 23 Apr 2007 11:02:17 -0600 (Mountain Daylight Time)

> I am having troubles to prepare the snapshots for mm_pbsa
> analysis. I have the trajectory file and the corresponding prmtop file, wich I
> can visualize in VMD without problems. The point is that after striping the
> waters and ions with ptraj, and obtaining the new desolvated and deionized
> prmtop files, when I try to check the new trajectory, I find that the ligand
> atoms are all missplaced, with corrupted binding distances, angles and lenghts.

Usually this is a problem with the box information, either still being
present when not expected or not being present when expected. The first
frame/snapshot will look good and all subsequent will be offset.

ptraj by default (and stupidly) automatically outputs box information;
MM-PBSA can read box information or not, depending on the "BOX" keyword.

If you are stripping, generally you want "nobox" appended to the trajout

strip :WAT
trajout mdcrd.strip nobox
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Received on Wed Apr 25 2007 - 06:07:21 PDT
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