AMBER: Nudget Elastic Band query

From: Francesco Pietra <>
Date: Thu, 5 Jul 2007 10:43:43 -0700 (PDT)

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

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.


francesco pietra

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Received on Sun Jul 08 2007 - 06:07:26 PDT
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