Re: [AMBER] how to obtain 4x4x1.1nm water; how to add polarizable models

From: David A Case <>
Date: Mon, 14 Mar 2011 11:16:30 -0400

On Mon, Mar 14, 2011, gromacs wrote:

> Can anybody tell me how to get 4x4x1.1 box, and then fill this box with
> water (e.g. pol3)?

Amber doesn't have any direct commands to create a box of a certain dimension
filled with water. You might try packmol or some related program. Once you
have a pdb-format file with the coordinates, then you can load that into leap,
use setBox to set the box dimensions, and set up the pol3 potential as
described in the Users' Manual.

> and how can i add polarizable models which is not existed in AMBER
> 9 (e.g. i need other polarizable water models and other polarizable
> ions)? What files should i modify?

This is not an easy task. If you want to implement potentials not
supported by Amber, you will need to learn a lot, and be prepared to
modify the programs. Since you seem to have only a little experience with
Amber for the potentials we *do* support, plan on doing a lot of reading
and experimenting: this is not something the mailing list will be able to
help out much with.


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Received on Mon Mar 14 2011 - 08:30:06 PDT
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