Thanks Dan. I understand what you mean now.
Lekpa
On 9/21/10, Daniel Sindhikara <sindhikara.gmail.com> wrote:
> 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
>> >
>> _______________________________________________
>> 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/
> --
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Sep 21 2010 - 08:00:07 PDT
