AMBER Archive (2008)

Subject: Re: AMBER: how to add new solvent type in Amber

From: David A. Case (
Date: Wed Dec 10 2008 - 17:18:56 CST

On Tue, Dec 09, 2008, iccy liu wrote:
> I have a question about adding a new solvent type in
> Amber. I did search the manual and tutorials and couldn't find the procedure
> to do it. Can anyone help me? Since my solvent is a new type of molecule,
> I followed the tutorial 4 and build a single molecule pdb, then using
> antechamber to generate single solvent molecule *.prepin and *.frcmod
> file. What is next step should I do? I would like to build a solvent box and
> loaded it later. what kind of files is needed and how to load the new type
> solvent box? Any input will be high appreciated. Thanks a lot!

Two approaches: you can just solvate with a single molecule, rather than a
box. This doesn't create a great starting structure, but it can be good
enough if you follow this with careful equilibration.

Or, you can try the packmol program to create a starting structure, then use
that. Just Google for "packmol".


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