I think you can do that also. You also do the calculation by considering all the residues. Then compare all the results (per residue and overall) to what you are expecting or the reported ones, if any.
Best,
Satyajit
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________________________________
From: Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in>
Sent: Monday, November 6, 2023 12:28:41 PM
To: SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
Cc: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Rdf calculation:
I mean I dont need to provide all key residue IDs same time ?
On Mon, Nov 6, 2023, 12:23 SATYAJIT KHATUA <satyajitkhatua09.gmail.com<mailto:satyajitkhatua09.gmail.com>> wrote:
Do it per residue wise and see if that is what you try to interpret from the calculations.
Best,
Satyajit
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https://aka.ms/AAb9ysg>
________________________________
From: Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in<mailto:kankana.bhattacharjee_phd21.ashoka.edu.in>>
Sent: Monday, November 6, 2023 12:17:15 PM
To: SATYAJIT KHATUA <satyajitkhatua09.gmail.com<mailto:satyajitkhatua09.gmail.com>>
Cc: AMBER Mailing List <amber.ambermd.org<mailto: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 - 23:30:01 PST
