Date: Mon, 6 Nov 2023 08:33:06 +0000
Looks ok to me.
________________________________
From: Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in>
Sent: Monday, November 6, 2023 2:01:45 pm
To: SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
Cc: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Rdf calculation:
For multiple amnio acid resides,
I have used something like this:
radial :WAT.O :1,2,3,4,5 (Lets say solute mask IDs) 0.5 15 noimage volume out rdf.dat. Is it correct ?
[Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> Sender notified by
Mailtrack<https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> 11/06/23, 02:00:19 PM
On Mon, Nov 6, 2023 at 1:34 PM Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in<mailto:kankana.bhattacharjee_phd21.ashoka.edu.in>> wrote:
yes. I have not specified the keyword. It worked.
[Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> Sender notified by
Mailtrack<https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> 11/06/23, 01:34:24 PM
On Mon, Nov 6, 2023 at 1:29 PM SATYAJIT KHATUA <satyajitkhatua09.gmail.com<mailto:satyajitkhatua09.gmail.com>> wrote:
You don't have to specify spacing and maximum. Just feed the value to the command line.
Get Outlook for Android<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 1:27:24 PM
To: SATYAJIT KHATUA <satyajitkhatua09.gmail.com<mailto:satyajitkhatua09.gmail.com>>
Cc: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Subject: Fwd: [AMBER] Rdf calculation:
Ok. Then, the command line will be:
radial :WAT.O :solute mask spacing 0.5 maximum 15.0 noimage volume out rdf.dat ?
---------- Forwarded message ---------
From: SATYAJIT KHATUA <satyajitkhatua09.gmail.com<mailto:satyajitkhatua09.gmail.com>>
Date: Mon, Nov 6, 2023 at 1:24 PM
Subject: Re: [AMBER] Rdf calculation:
To: Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in<mailto:kankana.bhattacharjee_phd21.ashoka.edu.in>>
Cc: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
I forgot. Yes, you have to specify the bin spacing and max bin value.
For testing make it something like bin spacing 0.5 and max bin 15.0
________________________________
From: Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in<mailto:kankana.bhattacharjee_phd21.ashoka.edu.in>>
Sent: Monday, November 6, 2023 1:21:17 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:
How can I specify bin spacing and maximum bin value ?
[Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> Sender notified by
Mailtrack<https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> 11/06/23, 01:20:47 PM
On Mon, Nov 6, 2023 at 1:19 PM Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in<mailto:kankana.bhattacharjee_phd21.ashoka.edu.in>> wrote:
After executing the command, I have found the error:
Error: Radial: No spacing argument or arg < 0.
I am not getting it. Kindly help
[Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> Sender notified by
Mailtrack<https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> 11/06/23, 01:19:22 PM
On Mon, Nov 6, 2023 at 1:14 PM Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in<mailto:kankana.bhattacharjee_phd21.ashoka.edu.in>> wrote:
Ok. Thanks.
[Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> Sender notified by
Mailtrack<https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> 11/06/23, 01:14:46 PM
On Mon, Nov 6, 2023 at 1:14 PM SATYAJIT KHATUA <satyajitkhatua09.gmail.com<mailto:satyajitkhatua09.gmail.com>> wrote:
No that is not required.
Get Outlook for Android<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 1:13:28 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:
Ok. No need to put " " in the mask options while specifying atom type/resids ?
[Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> Sender notified by
Mailtrack<https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> 11/06/23, 01:12:55 PM
On Mon, Nov 6, 2023 at 1:12 PM SATYAJIT KHATUA <satyajitkhatua09.gmail.com<mailto:satyajitkhatua09.gmail.com>> wrote:
Provide the command as something like
radial :WAT.O :solute_mask noimage volume out rdf.dat
________________________________
From: Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in<mailto:kankana.bhattacharjee_phd21.ashoka.edu.in>>
Sent: Monday, November 6, 2023 1:07:33 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:
So, residue ID is resolved. I have cross-checked with my solvated.pdb file.
So, should I have to use radial tool as:
radial ":WAT.O" "solutemask" noimage volume out rdf.dat ?
[Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> Sender notified by
Mailtrack<https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> 11/06/23, 01:03:56 PM
On Mon, Nov 6, 2023 at 12:48 PM SATYAJIT KHATUA <satyajitkhatua09.gmail.com<mailto:satyajitkhatua09.gmail.com>> wrote:
You have to add a volume keyword. You give original residue I'd of your amino acids. The ones you have in your solvated pdb file. It is not that hard to compare the residue I'd from vmd and the solvated pdb file. Extract those I'd and give it as solute mask
Get Outlook for Android<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 12:38:54 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:
Ok. Thanks.
The command line for RDF if I try with: radial ":WAT.O" "solute Mask" nointramol out rdf.dat. Is it the right one ?
One thing I would like to know, I found out the key residues from vmd. VMD provides residue name and resid (residue number +1), which number should I provide in cpptraj as mask ?
[Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> Sender notified by
Mailtrack<https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> 11/06/23, 12:38:39 PM
On Mon, Nov 6, 2023 at 12:32 PM SATYAJIT KHATUA <satyajitkhatua09.gmail.com<mailto:satyajitkhatua09.gmail.com>> wrote:
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
Get Outlook for Android<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 12:28:41 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:
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
Get Outlook for Android<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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org<mailto:AMBER.ambermd.org>
http://lists.ambermd.org/mailman/listinfo/amber
[Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> Sender notified by
Mailtrack<https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> 11/06/23, 01:26:54 PM
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
(image/gif attachment: image.gif)
