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".
...dac
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Received on Fri Dec 12 2008 - 01:12:37 PST
