AMBER: Simulated annealing - Nudget Elastic Band

From: Francesco Pietra <>
Date: Wed, 4 Jul 2007 00:01:58 -0700 (PDT)

I carried out the Nudget-Elastic-Band tutorial on N&#8209;acetyl&#8209;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

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

8:00? 8:25? 8:40? Find a flick in no time
with the Yahoo! Search movie showtime shortcut.
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Jul 08 2007 - 06:07:03 PDT
Custom Search