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 )
James 2013/4/6 Justin Lemkul <jalem...@vt.edu> > On Sat, Apr 6, 2013 at 10:46 AM, Albert <mailmd2...@gmail.com> wrote: > > > On 04/06/2013 04:29 PM, Justin Lemkul wrote: > > > >> And what was your basis for that decision? What makes you think that > >> AMBER99 can even be combined with the Berger lipid force field? > >> > >> -Justin > >> > > > > > > I think he probably read this paper which suggest the combination of > Amber > > FF and Berger lipids FF: > > > > http://pubs.acs.org/doi/abs/**10.1021/ct200491c< > http://pubs.acs.org/doi/abs/10.1021/ct200491c> > > > > Fair enough. I wasn't aware of that one. But if that's the case, then I > suggest James have another read through it, since the cutoffs are described > explicitly, thus answering his original question. > > -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 > -- 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