Re: AMBER: Simulated annealing - Nudget Elastic Band

From: Carlos Simmerling <>
Date: Wed, 4 Jul 2007 06:39:10 -0400

it's not clear what conformatinoal coordinates you want to explore-
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
> =========================
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Jul 08 2007 - 06:07:05 PDT
Custom Search