Hi Daniel,
I am interested in calculating preferential interaction coefficients of ligand(in my case I have randomly placed 10 molecules around the protein).
I am interested in knowing if this particular ligand prefers to interact/be near the surface or prefers to be in the bulk (excluded).
In order to do this, I need to first define what is local or bulk domain for my system.
probably,I will try doing the following:
I will calculate for varying r (radius from protein surface), the number of molecules interacting. At some point, this interaction will flatten, that will most likely be the cut off.
Do you have some other suggestions ?
Regards
Sowmya
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Tuesday, March 28, 2017 7:16 PM
To: AMBER Mailing List
Subject: Re: [AMBER] RDF plot
OK, the peptides used in the study you point out (triglycine and
glycine betaine aka trimethylglycine) are *very* small, on the order
of 20 atoms. Therefore, all atoms are relatively well-solvated and
comparatively homogeneous, so they don't really have the issue that I
described. You are trying to take the RDF of a much, much larger
number of atoms (it comprises 40 residues, which I estimate is
probably 600 or so atoms) which will be much more heterogeneous and so
the RDF will suffer from the issues I previously described.
What exactly are you trying to show? It is likely there is another
analysis that will serve your purposes much better.
-Dan
On Tue, Mar 28, 2017 at 1:04 PM, Sowmya Indrakumar <soemya.kemi.dtu.dk> wrote:
> Apologies for sending half the information. Below is the title of the paper :
>
> 'Preferential Interactions between Small Solutes and the Protein Backbone: A Computational Analysis'
>
> Thanks
> Regards
> Sowmya
>
> _
> _______________________________________
> From: Daniel Roe [daniel.r.roe.gmail.com]
> Sent: Tuesday, March 28, 2017 6:55 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] RDF plot
>
> 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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>>
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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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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 - 10:30:06 PDT
