AMBER Archive (2008)

Subject: Re: AMBER: solvate box : buffer list

From: David A. Case (case_at_scripps.edu)
Date: Tue Jun 03 2008 - 13:22:16 CDT

On Tue, Jun 03, 2008, fatima.chami_at_durham.ac.uk wrote:
>
> I tried to solvatebox command with a given buffer list but tleap does not
> recognize the list ..is my synta wrong ??

Yes: lists need to look like this: {1 0 1}
(See section 3.2.3 of the Amber9 or AmberTools Users' Manual).

Note that that it is not clear to me that LEaP will perform as you expect(?)
with such a small buffer. The result might be very erratic.

>
> solvateBox columTbW3 TIP3PBOX 1 0 1
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu