Hi Ming,
In that case, I should atleast get it for a specific atom in a given residue. It still fails.
I am aware this can be used for protein as whole.
Regards
Sowmya
________________________________________
From: Ming Tang [m21.tang.qut.edu.au]
Sent: Tuesday, March 28, 2017 12:41 PM
To: AMBER Mailing List
Subject: Re: [AMBER] RDF plot
Hi,
>From my understanding, RDFs are only for specific atoms as water distribution is different around different atoms even in the same residue.
-----Original Message-----
From: Sowmya Indrakumar [mailto:soemya.kemi.dtu.dk]
Sent: Tuesday, 28 March 2017 8:36 PM
To: amber.ambermd.org
Subject: [AMBER] RDF plot
Dear All,
I am trying to calculate water/solute-peptide radial distribution function g(r). I was successful in calculating the same for the water-water system and water-Cl-. (see the attached file rdf.png).
1) radial *.rdf 0.5 15 :WAT.O :WAT.O volume
2) radial *.rdf 0.5 15 :WAT.O :Cl- volume
But I am unable to calculate w.r.t to protein or any specific residue in the protein. (see attached file: protein) I used the below command:
3) radial *.rdf 0.5 15 :WAT.O :1-40.CA,C,N,O volume
Kindly, let me know.
Regards
Sowmya
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Received on Tue Mar 28 2017 - 04:00:04 PDT
