Hey Mark, Nihal, On Tue, Sep 13, 2011 at 2:06 AM, Mark Abraham <mark.abra...@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. Cheers, Tsjerk -- 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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
