AMBER Archive (2006)

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

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Tue Aug 08 2006 - 07:43:47 CDT

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