[gmx-users] V(R) around protein

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Sep 15 21:37:11 CEST 2011

Hey Mark, Nihal,

On Tue, Sep 13, 2011 at 2:06 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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.

That won't work. A probe with infinite radius will give the convex
volume of the peptide, not the volume that is desired. You could
change the atomic radii to get the volume. There is also another way,
which is not completely trivial. Yet it lies along the lines of a tool
I have, which could be modified to suit the need. If you're
interested, you can contact me off list for more information.



Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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