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

From: Carlos Simmerling <>
Date: Mon, 07 Mar 2005 08:29:14 -0500

It isn't clear what you are doing. when you run vmd, do you load a prmtop
that has no water and no Na+? Since you modified the trajectory you cannot
use the original prmtop anymore.

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:

scopio wrote:

> 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
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Received on Mon Mar 07 2005 - 13:53:00 PST
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