AMBER: A problem about removing waters and counterions by ptraj

From: scopio <>
Date: Mon, 07 Mar 2005 20:28:19 +0800

Dear Amber users:

I am carring on several similar MD calculations with ligand binding to
different interesing sites. And I meet a problem when using ptraj to
process one of the trajectory whileas others are OK when doing the same

What I want to do is just to remove waters and counterions from the
trojectories. I found when I tried to remove Na+ from the trajectory, each
frame in the outputted trajctory was in disorder when displayed in VMD. I
also checked the initial trajectory file, it looks well.

The ptraj script is as below:

trajin test.traj.gz
strip :WAT,Na+
trajout test.out.traj.gz nobox

Attached please find test.tgz, a file containg topology, trajctory and
ptraj script file.

I hope anyone of you could tell me what's the problem with my file/script.
Thanks in advance!

Best Regards!


JunJun Liu
College of Chemistry
Central China Normal University
WuHan   430079
P.R. China

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Received on Mon Mar 07 2005 - 12:53:02 PST
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