Hi! There is support in gromacs for gb calculations. However, I'm currently investigating some recent reports about unstable simulations (unfolding proteins), so my advice is to use the code with caution.
Thanks /Per 30 nov 2011 kl. 20:04 skrev "R.S.K.Vijayan" <biovija...@gmail.com>: > Dear Gromacs users > > Is there any script that does a PB or GB calculation to perform a > MM/PB(GB)SA free energy calculation in Gromacs. Similar to the MMPBSA.py > script available in Amber. I find a similar question raised by a user a > couple of years back. Any successful implementation???? > > > Vijayan.R > > > > On Wed, Nov 30, 2011 at 1:26 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > κΉνμ wrote: > Dear Experts, > Hi, > Is there any tools in gromacs to get "Hydrophobic cores" of protein ? > > > I suppose that depends on what your definition is, but in all likelihood no, > not directly. A program like g_sas can give you nonpolar and polar surface > areas as well as volumes and surface atoms, which, through crafty use of > index groups, may provide you with something useful. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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
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