AMBER Archive (2008)

Subject: Re: AMBER: solvate box : buffer list

From: fatima.chami_at_durham.ac.uk
Date: Wed Jun 04 2008 - 05:07:06 CDT

Quoting "David A. Case" <case_at_scripps.edu>:

>
> 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).
Dear David,
Thanks for replying.

>
> 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.
>
I am starting from a small buffer to work out the concentration... I would like
to reach (30 -35 % wt.).
is there a way to work around this

best wishes
Fatima
> >
> > solvateBox columTbW3 TIP3PBOX 1 0 1
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