[gmx-users] amber99 with berger's lipids

Justin Lemkul jalemkul at vt.edu
Mon Apr 8 15:06:56 CEST 2013

On Mon, Apr 8, 2013 at 7:50 AM, James Starlight <jmsstarlight at 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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)


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