Re: [AMBER] Replacing water with oxygen molecules

From: David A Case <>
Date: Mon, 2 Mar 2015 20:29:57 -0500

On Mon, Mar 02, 2015, Shukla, Saurabh wrote:

> I want to replace around 200 water molecules around my protein by
> oxygen molecules. I have created .lib and .frcmod files for the oxygen
> molecule.
> I can’t find the method of replacement. My pdb does not have oxygen
> molecules. I am introducing them. Please suggest the commands/way to do
> it.

This is not a "standard" modeling operation that Amber supports. Only
you know how you want to choose which 200 waters (out of the thousands
that are there) to replace. Once you choose the waters to replace, just
delete them from your PDB file, and replace with oxygen molecules at the
same position -- orientation probably won't matter, since they will rotate
fairly quickly as you equilibrate.

...good luck....dac

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Received on Mon Mar 02 2015 - 18:00:03 PST
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