Re: [AMBER] How to have a certain number of water molecules?

From: David Case <>
Date: Tue, 20 Dec 2016 13:15:35 -0500

On Tue, Dec 20, 2016, Azade Yazdan Yar wrote:

> I am trying to build several boxes which contain different residues. I
> would like to have the same number of water molecules in all boxes.
> Is there any easy way to do this? (the 'solvatebox' command is not very
> number-orientated)

You can use Amber's AddToBox program, or "packmol". I think both will do what
you want.

> And my second question is: Imagine I have used the 'solvatebox' command on
> my residue. Is there any way to now undo this? e.g. remove the added water
> molecules from the box?

ParmEd can do this.


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Received on Tue Dec 20 2016 - 10:30:02 PST
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