AMBER Archive (2006)

Subject: Re: AMBER: How to calculate RDF based on the center of mass of specific solute atoms?

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Sun Oct 15 2006 - 23:36:25 CDT

I am not sure whether I understand you fully. How
about Ptraj distance?

Best regards.

Fenghui Fan

--- Xioling Chuang <xioling_c_at_hotmail.com> wrote:

> Dear All,
>
> To calculate RDF from DNA atoms to water (oxygen
> atom) using command
>
> radial filename 0.05 8.5 :WAT_at_O :1-20
> closest density 0.033456
>
> as I understood, PTRAJ will calculate RDF based on
> DNA surface. My question
> is that how to calculate the RDF based on center of
> mass of specific solute
> atoms (e.g. center of mass of only residue 1)?
> many thanks in advance for your suggestion.
>
> Regards,
> Xioling
>
>
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