Re: [AMBER] Creating a new Solvatebox

From: David A. Case <>
Date: Tue, 23 Jul 2013 11:02:01 -0400

On Mon, Jul 22, 2013, Chinthaka Ratnaweera wrote:
> Once the saveoff command make a box 'unit' ( I guess I have to save it as
> a lib file), inorder to use that unit to solvate the protein, do I have to
> use loadoff command to open it and give this unit name as second argument
> in solvatebox command?


> Does size of the solvate box matters when setup the initial box using
> packmol?

It's not a big deal which size you choose. Most of the "standard" boxes
are really smaller than they should be (some were made back in the 1980s when
computers were much slower.) The solvateBox and solvateOct routines will
replicate and truncate boxes as needed. Something on the order of 1000
ethanol molecules should be fine.

...good luck....dac

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Received on Tue Jul 23 2013 - 08:30:03 PDT
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