AMBER Archive (2004)

Subject: Re: AMBER: (no subject)

From: Anselm Horn (Anselm.Horn_at_biochem.uni-erlangen.de)
Date: Wed Sep 29 2004 - 10:00:43 CDT

Hi Rasha,

> Hi, I'm a new user of AMBER , and I need to know how to build a topology
> and coordinate files for pure water box. I know how to solvate any
> molecule in a water box, but my main concern is to get the water box by
> itself without any thing being solvated inside it.
> Rasha
a quick workaround would be to solvate one molecule of water within the WATBOX216.
You need just a one-line pdb file, e.g.

HETATM 1575 O HOH 402 0.000 0.000 0.000 1.00 1.00

Then use leap for the creation of a water box around that:
source leaprc.ff99
p = loadpdb water.pdb
solvatebox p WATBOX216 10.0 1.0
saveamberparm p water.top water.crd

Regards,

Anselm 

-- 
Abteilung f. Bioinformatik
Institut f. Biochemie
Friedrich-Alexander-Universitaet Erlangen-Nuernberg
Fahrstrasse 17
91054 Erlangen
Tel.: +49-9131-85-24682
Germany

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