[gmx-users] V(R) around protein

[Mark Abraham]

On 13/09/2011 9:47 AM, E. Nihal Korkmaz wrote:
> And I don't think g_sas would do what i want. It calculates the volume 
> of the protein itself. I am interested in the V of space at a distance 
> R from the surface of the protein, excluding the volume of the 
> protein. In other words, i need the surface accessible volume as a 
> function of distance from the surface of the protein.

So do two calculations with different probe radii.

Mark

>
>
> Nihal
>
> On Mon, Sep 12, 2011 at 6:42 PM, E. Nihal Korkmaz 
> <enihalkorkmaz at gmail.com <mailto:enihalkorkmaz at gmail.com>> wrote:
>
>     R is any distance from the surface of the protein.
>
>
>     On Mon, Sep 12, 2011 at 6:31 PM, Mark Abraham
>     <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>         On 13/09/2011 9:29 AM, E. Nihal Korkmaz wrote:
>
>             Dear all,
>
>             Is there any function to get the Volume around a
>             peptide/protein as a function of R?
>             The problem is g_rdf -surf doesn't have a volume
>             correction factor, so my aim is to apply a volume
>             correction factor manually by having V(R) around the protein.
>
>
>         You haven't said what R is, but g_sas will calculate some volumes.
>
>         Mark
>         -- 
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>
>     -- 
>     Elif Nihal Korkmaz
>
>     Research Assistant
>     University of Wisconsin - Biophysics
>     Member of Qiang Cui & Thomas Record Labs
>     1101 University Ave, Rm. 8359
>     Madison, WI 53706
>     Phone: 608-265-3644 <tel:608-265-3644>
>     Email: korkmaz at wisc.edu <mailto:korkmaz at wisc.edu>
>
>
>
>
>
> -- 
> Elif Nihal Korkmaz
>
> Research Assistant
> University of Wisconsin - Biophysics
> Member of Qiang Cui & Thomas Record Labs
> 1101 University Ave, Rm. 8359
> Madison, WI 53706
> Phone:  608-265-3644
> Email: korkmaz at wisc.edu <mailto:korkmaz at wisc.edu>
>
>
>
>

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