Hi,
Have you tried to specify just one residue in the protein? Your mask (:
1-40.CA,C,N,O) is very large -40 residues-, and I’d expect to see a diffuse pdf, as you show. I believe cpptraj is centering the rdf in the center of mass of the mask, and then counting from there. However, this center is too buried in the protein.
—
Gustavo Seabra.
> Em 28 de mar de 2017, à(s) 07:35, Sowmya Indrakumar <soemya.kemi.dtu.dk> escreveu:
>
> 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
>
> <rdf.png><protein>_______________________________________________
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Received on Tue Mar 28 2017 - 04:30:03 PDT
