On Tue, Mar 28, 2017 at 12:18 PM, Sowmya Indrakumar <soemya.kemi.dtu.dk> wrote:
> In some papers, they have shown g(r) of solute around the peptide : Biochemistry, Vol. 49, No. 9, 2010
Could you narrow it down a bit for me - maybe give me the page number,
DOI, title, authors etc? That issue contains a lot of articles and I'd
rather not go through them one by one and guess which one you mean.
-Dan
>
> 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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--
-------------------------
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 - 10:00:03 PDT
