AMBER Archive (2006)

Subject: Re: AMBER: cutting the box after "solvatebox"

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Tue Aug 08 2006 - 07:52:39 CDT

I want to remove the waters also ....

I looked the the box command in ptraj but it doesnt remove waters ...

Carlos Simmerling wrote:

> you can modify the box dimensions directly in the coordinate file.
> do you just want to change the box edge or actually remove some
> of the water too?
>
>
>
> Vlad Cojocaru wrote:
>
>> Dear Amber users,
>>
>> I created a box around a solute (loaded as pdb) using "solvatebox sol
>> TIP3PBOX {0 20 0}". However, I need to cut out from this box about 5A
>> from each side of the x and y directions and about 10A from 1 side of
>> the z direction. Is there any tool in Amber that can do that?
>>
>> Thanks
>>
>> vlad
>>
>>
>>
>>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> 

-- 
Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu