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 <enihalkork...@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.abra...@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@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-requ...@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: kork...@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: kork...@wisc.edu
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