Re: [AMBER] Rdf calculation:

Date: Mon, 6 Nov 2023 06:42:58 +0000


As solute mask you can give the amino acid residue I'd of your interest as one mask and give water O atom (:WAT.O) as the solvent mask. Most of the times, the interest lies on the calculation of pair correlation in terms of water O atom only.


From: Kankana Bhattacharjee via AMBER <>
Sent: Monday, November 6, 2023 11:49:01 am
To: AMBER Mailing List <>
Subject: [AMBER] Rdf calculation:

Dear AMBER users,

I would like to compute rdf of water molecules with respect to key amino
residues. For that how can I define the solute and solvent mask ?
I have few amino acid residues as reference point should I have to mention
the residue ID of every amino acids in solute mask ?
For solvent mask if I give ":WAT" will that work ?
Your suggestion would be highly appreciated.

Thanks & Regards
Kankana Bhattacharjee
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Received on Sun Nov 05 2023 - 23:00:02 PST
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