Thanks Matt! I've seen some vmd tcl scripts using msms to get the surface area. However I think as gromacs using united atom, I need too change radii parameters or in a more simple way, add all hydrogen back before calculation....
Cheers Guang 2012/11/8, Matthew Zwier <mczw...@gmail.com>: > 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 > -- 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