Hi,
> Em 28 de mar de 2017, à(s) 09:49, Sowmya Indrakumar <soemya.kemi.dtu.dk> escreveu:
>
> I did try with one specific atom of a residue (see attached file), it does flatten to 1 but at larger distances.
Curiosity: which residue was it?
> When I reduce the mask :(1-4.CA), it still shows the integrated graph as earlier.
> Is there way to consider the entire peptide?
I imagine residues 1-4 may be buried in the peptide, so using them as center would not be much different than the previous situation.
How large is the water box around the protein? I imagine that you would need a large box and larger limits to your rdf. In any case, the diffuse rdf you see may be just right for such a large mask.
Gustavo.
> Thanks.
> REgards
> Sowmya
> ________________________________________
> From: Gustavo Seabra [gustavo.seabra.gmail.com]
> Sent: Tuesday, March 28, 2017 1:26 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] RDF plot
>
> Hi,
>
> Have you tried to specify just one residue in the protein? Your mask (:1-40.CA,C,N,O) is very large -40 residues-, and I’d expect to see a diffuse pdf, as you show. 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.
>
> —
> Gustavo Seabra.
>
>
>
>> Em 28 de mar de 2017, à(s) 07:35, Sowmya Indrakumar <soemya.kemi.dtu.dk> escreveu:
>>
>> Dear All,
>> I am trying to calculate water/solute-peptide radial distribution function g(r). I was successful in calculating the same for the water-water system and water-Cl-. (see the attached file rdf.png).
>>
>> 1) radial *.rdf 0.5 15 :WAT.O :WAT.O volume
>> 2) radial *.rdf 0.5 15 :WAT.O :Cl- volume
>>
>> But I am unable to calculate w.r.t to protein or any specific residue in the protein. (see attached file: protein)
>> I used the below command:
>>
>> 3) radial *.rdf 0.5 15 :WAT.O :1-40.CA,C,N,O volume
>>
>> Kindly, let me know.
>> Regards
>> Sowmya
>>
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Received on Tue Mar 28 2017 - 06:00:03 PDT
