On Mon, Apr 8, 2013 at 7:50 AM, James Starlight <jmsstarli...@gmail.com>wrote:
> In literature I found that the ussage of 1.0 cutoffs should give good > results but in the antechamber manual I've seen that usages of 1.2 cutoofs > ( with GAFF) should be used. So what cut-offs should I use for > protein-ligand complexes done in amber ? (assuming that I simulate my > system in the berger lipids ) > > > Do a few test runs and see. I would think the cutoff value would more strongly affect the lipids, not the ligand, whose interactions are comparatively few and relatively local. If you use the Verlet cutoff scheme in version 4.6, it's largely irrelevant since there will not be any "missed" interactions either way. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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
