Date: Mon, 6 Nov 2023 07:59:13 +0000
You don't have to specify spacing and maximum. Just feed the value to the command line.
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From: Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in>
Sent: Monday, November 6, 2023 1:27:24 PM
To: SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
Cc: AMBER Mailing List <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 ?
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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
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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 ?
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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
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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.
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On Mon, Nov 6, 2023 at 1:14 PM SATYAJIT KHATUA <satyajitkhatua09.gmail.com<mailto:satyajitkhatua09.gmail.com>> wrote:
No that is not required.
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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 ?
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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
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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 ?
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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
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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 ?
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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
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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
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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
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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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