Re: [AMBER] 2D radial distribution function

From: Daniel Sindhikara <sindhikara.gmail.com>
Date: Tue, 21 Sep 2010 20:40:24 +0900

Lekpa,
  Ok it looks pretty straightforward. I assume you want to calculate the 2d
rdf from a trajectory you already ran right?
If so, you can just run ptraj to extract out those two distances you're
looking for. Paste them together, then calculate the 2D
histogram using a graphics program or one you wrote yourself. Essentially
this is the same thing you would do to create a ramachandran plot.
Hope I was clear. Does this make sense?

--Dan


On Tue, Sep 21, 2010 at 8:08 PM, Lekpa Duukori <duukori.gmail.com> wrote:

> Hello Dan,
>
> Sorry about the bad links. This should be better
>
>
> http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TGP-3YB4DPX-3&_user=10&_coverDate=04/30/1999&_rdoc=3&_fmt=high&_orig=browse&_origin=browse&_zone=rslt_list_item&_srch=doc-info(%23toc%235260%231999%23999829997%23153829%23FLA%23display%23Volume)&_cdi=5260&_sort=d&_docanchor=&_ct=5&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=c6b510416c0eb16fdf0135e542a705c6&searchtype=a<http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TGP-3YB4DPX-3&_user=10&_coverDate=04/30/1999&_rdoc=3&_fmt=high&_orig=browse&_origin=browse&_zone=rslt_list_item&_srch=doc-info%28%23toc%235260%231999%23999829997%23153829%23FLA%23display%23Volume%29&_cdi=5260&_sort=d&_docanchor=&_ct=5&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=c6b510416c0eb16fdf0135e542a705c6&searchtype=a>
> <
> http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TGP-3YB4DPX-3&_user=10&_coverDate=04/30/1999&_rdoc=3&_fmt=high&_orig=browse&_origin=browse&_zone=rslt_list_item&_srch=doc-info%28%23toc%235260%231999%23999829997%23153829%23FLA%23display%23Volume%29&_cdi=5260&_sort=d&_docanchor=&_ct=5&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=c6b510416c0eb16fdf0135e542a705c6&searchtype=a
> >
>
>
> 2D rdf uses two reference points eg N --- Ow ---- O where looking at
> distribution between N -- Ow and Ow -- O simultaneously.
>
> Yes my coordinates are in AMBER format but I don't understand exactly how
> this histograming should work.
>
> Lekpa
> On Tue, Sep 21, 2010 at 4:40 AM, Daniel Sindhikara <sindhikara.gmail.com
> >wrote:
>
> > Hi,
> > It's hard to tell what exactly you're looking for for two reasons:
> > 1) Your links seem to be related to your institution (can you find a
> > permalink?)
> > 2) What do you mean by 2D RDF? you mean between two different pairs?
> >
> > If the coordinates are calculable in ptraj (which is likely) then you can
> > just run ptraj and 2D histogram the results.
> >
> >
> > --Dan
> >
> > On Tue, Sep 21, 2010 at 6:36 PM, Lekpa Duukori <duukori.gmail.com>
> wrote:
> >
> > > Hi everyone,
> > >
> > > Does anyone know of a software that can calculate 2D radial
> distribution
> > > functions as described in
> > >
> > > *The mean hydration of carbohydrates as studied by normalized
> > > two-dimensional radial pair
> > > distributions<
> > >
> >
> http://0-apps.isiknowledge.com.darius.uleth.ca/full_record.do?product=WOS&qid=15&SID=4CfNkjLfobNIh86blda&doc=1&colname=WOS
> > > >
> > > *
> > > Andersson C<
> > >
> >
> http://0-apps.isiknowledge.com.darius.uleth.ca/DaisyOneClickSearch.do?product=WOS&search_mode=DaisyOneClickSearch&db_id=&SID=4CfNkjLfobNIh86blda&name=Andersson%20C&ut=000085179400003&pos=1
> > > >
> > > , Engelsen SB<
> > >
> >
> http://0-apps.isiknowledge.com.darius.uleth.ca/DaisyOneClickSearch.do?product=WOS&search_mode=DaisyOneClickSearch&db_id=&SID=4CfNkjLfobNIh86blda&name=Engelsen%20SB&ut=000085179400003&pos=2
> > > >
> > > *JOURNAL OF MOLECULAR GRAPHICS & MODELLING* Volume: 17 Issue: 2 Pages:
> > > 101-+
> > > Published: APR 1999
> > >
> > > Thanks
> > >
> > > Lekpa
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Dr. Daniel J. Sindhikara
> > Institute for Molecular Science
> > E-mail: sindhikara.gmail.com
> > Website: http://sites.google.com/site/dansindhikara/
> > --
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>



-- 
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
--
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Received on Tue Sep 21 2010 - 05:00:07 PDT
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