Re: AMBER: Simulated annealing - Nudget Elastic Band

From: Francesco Pietra <>
Date: Wed, 4 Jul 2007 06:13:41 -0700 (PDT)

When there is more than one chirality axis, or just one chirality axis plus one
chiral center (such as a chiral carbon center), conformational inversions
(rotations) around the chirality axes generate diastereomers, such as in my
cases. My atropisomers have various stability, from ephemeral to isolatable on
the bench.

Energy barriers to such conformational inversions (measured from either CD or
opt rotation) are in my case around 24 kilocalories per mol in chloroform
solution, with first order kinetics. This should indicate how to set the
simulated annealing, on which I have no experience at all. Actually I am new at

The coordinates to explore concern specifically the two rings interconnected
through a carbon-carbon single bond (chirality axis). Though, this involves the
conformational change of interconnected other carbocycles, and there are
rotatable side chains. In other words, all coordinated should be monitored,
except the aromatic rings that save their planarity throughout.

So far, I succeeded in sampling the whole conformational space with such ff as
MMFF94 and an algorithm (BAKMDL) whereby all rotatables are systematically
rotated, while non-aromatic rings are opened and re-closed, though in vacuum.
Implicit solvent could be indicated, as dielectric constant, but it is not felt



--- Carlos Simmerling <> wrote:

> it's not clear what conformatinoal coordinates you want to explore-
> chirality
> inversions? rotatable bonds? the method that you choose to sample them
> depends much on the expected barrier heights.
> On 7/4/07, Francesco Pietra <> wrote:
> >
> > I carried out the Nudget-Elastic-Band tutorial on N‑acetyl‑alanine
> > methylamide as an introduction to conformational problems I am engaged
> > with on
> > novel natural products.
> >
> > Though, I am concerned with molecules that have no repeating units (thus
> > antechamber-gaff should be used to provide prmtop and inpcrd files) and
> > embody
> > chirality axes that involve conformational change of carbocyclic rings.
> > Thus
> > multidimensional energy surfaces are at issue.
> >
> > I have checked (following the procedures of the sustiva-antechamber
> > tutorial)
> > that antechamber-gaff can treat my molecules with little additional divcon
> > computing. I have found that partial charges differ much from those
> > calculated
> > for these molecules via HF-6-31G*; it was expected.
> >
> > Now, I wonder whether the above NEB example has already been extended to
> > multidimensional surfaces. In principle, I could follow the above NEB
> > tutorial
> > for a single chirality axis, which - if I understand the tutorial - would
> > pose
> > a restraint on all other parts of the molecule. That would be no solution
> > to my
> > problems.
> >
> > Is any unbiased (unbiased as to conformations) procedure already
> > established
> > for simulated annealing with multidimensional surfaces? Incidentally,
> > these my
> > problems can't be proficiently approached by mmff94-type molecular
> > mechanics
> > because the conformational behavior is solvent-dependent and the final
> > task is
> > the interaction of the natural product with a receptor. Though, I already
> > carried out a global-space conformational exploration by MM in vacuum.
> >
> > I understand that questions should be posed to Amber for specific
> > problems,
> > with command lines and error ensuing, though, my problem here is of
> > general
> > strategy. Simply, it is not clear to me if there is already a guideline -
> > no
> > matter how raw - before attempting by myself to find a viable way.
> >
> > Thanks for your understanding
> >
> > francesco pietra
> >
> > =========================

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Received on Sun Jul 08 2007 - 06:07:09 PDT
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