On Fri, Feb 5, 2016 at 5:31 PM, Krantzman, Kristin D <KrantzmanK.cofc.edu>
wrote:
> Hi Carlos and Jason,
> I have visualized the periodic images, and the protein does not appear to
> be interacting with itself.
> I have a question about the rdf. The rdf that I has structure, but the
> peaks are not well defined. Furthermore, the asymptotic value as the
> distance approaches the bulk is 0.9, not 1.0.
> I have used the command
> radial rad.dat 0.1 10.0 :WAT.O :ALA
> radial rad2.dat 0.1 10.0 :WAT.H1 :ALA
> radial rad3.dat 0.1 10.0 :WAT.H2 :ALA
> The polypeptide consists of 20 alanine residues, and it is not spherical.
>
​Since it's not globular, I would not expect the RDF that you calculated to
be as well-structured as, say, the RDF about the first alanine residue. I
think you may also need to use the "volume" keyword to have the RDF
approach 1, but I'm not positive on that. Try different options and see
what you get.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 05 2016 - 19:00:05 PST
