AMBER Archive (2008)

Subject: Re: AMBER: solvate box : buffer list

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

On Tue, Jun 03, 2008, wrote:
> I tried to solvatebox command with a given buffer list but tleap does not
> recognize the list 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
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