[AMBER] RDF plot

From: Sowmya Indrakumar <soemya.kemi.dtu.dk>
Date: Tue, 28 Mar 2017 10:35:39 +0000

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



_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

rdf.png
(image/png attachment: rdf.png)

Received on Tue Mar 28 2017 - 04:00:03 PDT
Custom Search