[gmx-users] amber99 with berger's lipids

[James Starlight]

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 <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
> 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
>
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