Hi Daniel,
Thank you for your response.
I did try using the center1, but it did not help. Also, thought about the normalisation issue, but using either density or volume flag, problem wasn't solved either.
In some papers, they have shown g(r) of solute around the peptide : Biochemistry, Vol. 49, No. 9, 2010
My interest is to define the two domain (local and bulk) w.r.t the protein surface for which I am interested in plotting the rdf to then decide on a cutoff to separate the two domains.
Kindly, let me know if you have some ideas on this.
Thanks in advance.
Regards
Sowmya
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Tuesday, March 28, 2017 3:59 PM
To: AMBER Mailing List
Subject: Re: [AMBER] RDF plot
On Tue, Mar 28, 2017 at 7:26 AM, Gustavo Seabra
<gustavo.seabra.gmail.com> wrote:
>
> 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.
Actually, by default cpptraj will output the averaged RDF of each atom
in the first (typically solvent) mask to each atom in the second
(typically solute) mask. This behavior can be modified by using the
'center1' / 'center2' keywords.
The reason to average many individual RDFs is to get better
statistics. What you seem to want is the RDF of the water to the
entire protein. This is problematic because the protein is far more
heterogeneous than water to water, water to ions, or water to a single
atom/specific functional group. As indicated before, some of your
atoms may be very solvent exposed and so the RDF will go to bulk
values in a shorter distance than atoms which are buried. When all
these get averaged together the details become lost. I would think
carefully about what you actually want to see and then tailor the RDF
to try to show that. For example, maybe you are interested in a
specific binding site - then just do the RDF to the center of atoms
surrounding the site, etc.
Hope this helps a little,
-Dan
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Mar 28 2017 - 09:30:02 PDT
