Many thanks Daniel. This very much sounds like what I wish to do. I shall give it a try.
Yes, the Ligands are a residue long.
Thank you once again.
Regards
Sowmya
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Tuesday, March 28, 2017 7:49 PM
To: AMBER Mailing List
Subject: Re: [AMBER] RDF plot
One thing you could do if your ligands are 1 residue each would be to
use the 'watershell' command to count how many instances of your
ligand are in the first/second solvation shells. The number of ligands
in bulk will be the total number of ligands (10) minus the number in
the second solvation shell (which includes the first solvation shell).
The defaults for first and second shell cutoffs are 3.4 and 5.0
Angstroms - you can adjust as needed. So something like the following
may work for you:
parm myparm.parm7
trajin mytraj.nc
watershell WS :1-40&!.H= <ligand mask>
run
bulk = 10 - WS[upper]
writedata ws.dat WS[upper] bulk
Again, this will *only* work if your ligands are only 1 residue long.
-Dan
On Tue, Mar 28, 2017 at 1:28 PM, Sowmya Indrakumar <soemya.kemi.dtu.dk> wrote:
> 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
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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 - 11:30:02 PDT
