[gmx-users] V(R) around protein
E. Nihal Korkmaz
enihalkorkmaz at gmail.com
Tue Sep 13 01:47:12 CEST 2011
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.
On Mon, Sep 12, 2011 at 6:42 PM, E. Nihal Korkmaz
<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>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.
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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
> Email: korkmaz at wisc.edu
Elif Nihal Korkmaz
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Email: korkmaz at wisc.edu
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