Re: AMBER: How to strip waters in trajectorie ?

From: simon whitehead <>
Date: Tue, 13 Jun 2006 09:24:37 +0100

Dear Jitrayut,

You can do this with the ptraj program. You can do this simply by using
the following input file;

trajin trajectorycoordfilename e.g. mdcrd
strip :WAT (assuming your waters have the residue name WAT)
trajout outputtrajectoryfilenameofyourchoice e.g. mdcrd.dry

You can then invoke ptraj in the following way;

ptraj prmtop < ptrajinputscript > ptrajinformationoutputfilename

This is quite a simple way of doing it but hope it is of some help. It
is explained in the ptraj section of the manual as well.


On Tue, 2006-06-13 at 02:50 +0700, jitrayut jitonnom wrote:
> Dear amber users
> I am a new users for amber so could anyone explain me about how to
> strip waters in a trajectorie file that obtained from explicit MD ? or
> maybe, what is an example of the script to do this ? These are my
> questions needed the answers from anyone.
> Thanks in advance for any suggestions
> Best regard
> Jitrayut

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Received on Wed Jun 14 2006 - 06:07:14 PDT
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