AMBER Archive (2004)

Subject: Re: AMBER: tmd questions

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Thu May 13 2004 - 06:41:31 CDT

perhaps you can save as PDB file and delete
the extra waters from 1, then reload it into
leap. I haven't done that myself, though.

----- Original Message -----
From: "hj zou" <hjzou_at_iris3.simm.ac.cn>
To: <amber_at_scripps.edu>
Sent: Wednesday, May 12, 2004 10:00 PM
Subject: AMBER: tmd questions

> Dear amber users£¬
> I wanna perform a TMD simulatin in amber 7.The initial and target
structures of protein are ready.But when I try to add waters by using
solvatebox,they have quite different numbers of waters in total which will
produce "inconsistent numbers...." error message while running TMD.So, how
can add same number of waters to both initial and target proteins?
> Any suggestions are highly appreciated.
> best regards
>
>
>
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