AMBER Archive (2005)

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

From: scopio (scopio_at_163.com)
Date: Mon Mar 07 2005 - 07:48:40 CST

Dear Dr.Simmerling

Thanks a lot! So silly I am. The pdb file I used for creating new topology
file contains Na+. Although I didn't add ions when producing new top file,
it does contain Na+ parameters.

Best Regards!

Liu

On Mon, 07 Mar 2005 08:29:14 -0500, Carlos Simmerling
<carlos_at_ilion.bio.sunysb.edu> wrote:

> 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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-- 
JunJun Liu

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

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