[gmx-users] V(R) around protein

[E. Nihal Korkmaz]

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.


Nihal

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.
>>
>> Mark
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>
>
>
>
> --
> 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

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110912/ea554cf5/attachment.html>