Do it per residue wise and see if that is what you try to interpret from the calculations.
Best,
Satyajit
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________________________________
From: Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in>
Sent: Monday, November 6, 2023 12:17:15 PM
To: SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
Cc: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Rdf calculation:
Amino acid residue ID of all ya any one ?
On Mon, Nov 6, 2023, 12:13 SATYAJIT KHATUA <satyajitkhatua09.gmail.com<mailto:satyajitkhatua09.gmail.com>> wrote:
Hi,
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.
Best,
Satyajit
________________________________
From: Kankana Bhattacharjee via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>>
Sent: Monday, November 6, 2023 11:49:01 am
To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
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 - 23:00:03 PST
