Hi Guang, Be careful with this tool. It's very fast and very good at what it's designed to do, but it does not appear to be designed to give accurate single-residue SASA (as you will read in the paper on the method employed). Definitely use g_sas for entire proteins or large cavities (it's blazing fast), but consider MSMS or DSSP for single-residue data.
Matt Zwier On Wed, Nov 7, 2012 at 1:26 AM, jia jia <jzg...@gmail.com> wrote: > Thanks! I've checked gromacs v 4.5.5 and got it. > Seems all version before 4.0.5 doen't have that information.. > > Cheers > Guang > > > 2012/11/7, Justin Lemkul <jalem...@vt.edu>: > > > > > > On 11/7/12 1:18 AM, jia jia wrote: > >> Dear gmx users: > >> So sorry for bother you. Does any one know what algorithm g_sas > >> use? There is no information about algorithm in help file, man page, > >> and code. I think gromos use naccess method but not sure gromacs use > >> the same one. > >> > > > > References are printed in the screen output when running g_sas. > > > > -Justin > > > > -- > > ======================================== > > > > Justin A. Lemkul, Ph.D. > > Research Scientist > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > ======================================== > > -- > > 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 > > > -- > 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 > -- 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
