Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling

From: Aron Broom <>
Date: Fri, 19 Oct 2012 14:30:18 -0400

Yeah, I see now what you are saying.

So you're not hoping to get the kinetics of the transition (since you've
added in this psuedo-bond), but rather just the equilibrium distribution of
the cis/trans forms?

I guess the most important thing then is to take the cis-structure, do the
RESP thing, and run MD on that. If it still favours the trans form, then
there is a bigger problem.

I suppose if you do see a bigger problem, and you are convinced its because
of hydrogen overlap, what you're suggesting is that AMBER is having this
problem because it is purely classical (at least the way you are running
it) and so the hydrogens aren't properly delocalized in a quantum sense and
so can't properly avoid one another? I'm not sure if this exists for
AMBER, but there are additions to other programs (like OpenMM / MMTK) that
allow for modelling of hydrogens as a delocalized cluster (perhaps using
path integral approaches). Maybe AMBER's QM approach could similarly be
used on the offending hydrogens? That's all quite speculative.


On Fri, Oct 19, 2012 at 1:11 PM, bio lab <> wrote:

> > The cis/trans states are controlled by a double-bond,
> > so that should mean that the only way to change between them
> > is for that double-bond to temporarily break no?
> Yes, exactly. This is what happens in reality: the molecule starts in trans
> conformation, sunlight (or UV light) temporarily breaks the double bond,
> the dihedral angle rotates, and finally the bond reforms when the molecule
> is in cis conformation.
> > Unless that isn't treated as a full double-bond and you modelled it
> > as some kind of peptide-bond like thing?
> Again, correct. I model it with a dihedral term with multiplicity 2 and a
> large force constant, similarly to the omega angle of a peptide bond.
> I think this is possible with MD, no?! Forget for a moment my specific
> case, and let’s imagine a simpler situation, in which there are no steric
> problems. For instance, the chain of a fatty acid with a single
> (unsaturated) double bond in the middle. I think one can use MD to model a
> cis-trans transition... this is unlikely to happen on a short time scale,
> but it could happen in MD at very high (although unrealistic) temperature.
> Please correct me if I am wrong on this.
> Now, back to my case. I agree that charges are not perfect and also the
> force constant should probably be adjusted, and this is what I was expected
> to work on. But then I stopped when I realized that the dihedral never ends
> up in cis (0°) and always returns to trans (180°) even when it has crossed
> the energy barrier (<90°). This is what I see happening at high-T. So I
> started to worry that charges and force constant would be only “premature
> optimization”, and there is a deeper problem with the modeling of the
> structure in the cis form, due to steric clash of atoms.
> Please notice that I still see this more as a problem of “static” modeling
> of the stable cis conformation, rather than of a correct dynamics of the
> transition between the two rotamers. I might be wrong on this, too.
> Thanks again for your attention.
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Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
AMBER mailing list
Received on Fri Oct 19 2012 - 12:00:03 PDT
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