Re: AMBER: Nudget Elastic Band query

From: Carlos Simmerling <>
Date: Thu, 5 Jul 2007 13:53:53 -0400

I don't have much experience with using NEB for this type of change, perhaps

if you just want relative free energies you might be better off with free
methods such as thermodynamic integration. NEB does not provide free
energies and is not yet implemented in Amber for use with explicit solvent.
If you can define a specific reaction coordinate you may use umbrella
If you want to try to reproduce a 10:90 ratio, you may want to spend some
time generating accurate parameters since this is a relatively small free
energy difference (a little over 1 kcal).

On 7/5/07, Francesco Pietra <> wrote:
> I fear that my answer to Carlos Simmerling about NEB was not dispatched
> correctly, or not dispatched at all.
> I said to have carried out tutorials antechamcer-sustiva and NBE with
> amber9,
> aimed at setting up simulated annealing for natural products.
> Antechamber-gaff,
> with little additional computing, proved able to deal with such large
> molecules
> without repeating units. Partial charges that I had determined by formal
> cutting of the molecule and applying HF-6-21G* methodology for RESP,
> differ
> substantially from those calculated by divcon-AM1.
> I was asked what I aimed to: querying about all coordinates, with only
> possible
> restraint for benzenoid rings. Inversion about chirality axes (which
> determines
> interconversion of diastereomers because of other chiral center present)
> faces
> a barrier of about 24 kcal/mol, values being solvent-dependent. Energy
> difference between disteromers involved in the conformational change is
> also
> solvent dependent. A 90:10 population was detected by NMR in chloroform
> solution.
> Simulation is intended for explicit solvents, also water. The final
> (future)
> aim is the study of interaction with receptors.
> I pointed out that I am new at simulated annealing, so that a modification
> of
> scripts for the NEB tutorial would be the best, if possible at all.
> Finally, I also said to have already carried out a global space
> conformational
> search by MM (MMFF94 ff) in vacuum. I also have computed the energy
> difference
> between disteromers in vacuum by ab initio methods, carrying out a
> vibrational
> analysis, correcting for ZPE and temperature, finding fair agreement with
> experimental observation for chloroform solution only.
> Tanks
> francesco pietra
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Received on Sun Jul 08 2007 - 06:07:27 PDT
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