AMBER Archive (2005)

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

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Mon Mar 07 2005 - 07:29:14 CST

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: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

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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