[gmx-users] amber99 with berger's lipids
jmsstarlight at gmail.com
Mon Apr 8 13:50:49 CEST 2013
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 )
2013/4/6 Justin Lemkul <jalemkul at vt.edu>
> On Sat, Apr 6, 2013 at 10:46 AM, Albert <mailmd2011 at 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
> > FF and Berger lipids FF:
> > 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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540)
> gmx-users mailing list gmx-users at gromacs.org
> * 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
More information about the gromacs.org_gmx-users