AMBER Archive (2005)

Subject: AMBER: A problem about removing waters and counterions by ptraj

From: scopio (scopio_at_163.com)
Date: Mon Mar 07 2005 - 06:28:19 CST

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
thing.

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!

liu 

-- 
JunJun Liu

College of Chemistry
Central China Normal University
WuHan   430079
P.R. China
  • application/x-gzip attachment: test.tgz

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