Re: AMBER: Creating an Ester with Antechamber/Gaff

From: David A. Case <>
Date: Fri, 2 Dec 2005 20:05:16 -0800

On Thu, Dec 01, 2005, John O'Mahony wrote:
> I'm attempting to simulate an ester compound, ethylene glycol
> dimethacrylate, preparing the file with Antechamber/ Gaff. The molecule
> looks fine, however when I attempt to minimise the structure, the 1-4
> EEL value looks extremely high, even after extensive minimisation.
> Building the structure up gradually, I observe a value of ~1.4 for the
> carboxylic acid form, up to ~36 for the methyl ester form and a value of
> 98 for the full ester (pdb file is attached, to show the structure).
> This causes us problems as we wish to solvate another molecule with many
> copies of this ester. Any ideas why these values are so high??

The magnitude of the 1-4 EEL term is not per-se meaningful, nor is there some
"ideal" value that it should have. What you need for minimization or dynamics
is that relative energies of different conformers of the *same molecule*
should be realistic. Comparing MM energies for different molecules is not

Bottom line: it is not clear that there is really any problem here. You may
have "high" contributions that are essentially constant for all reasonable
configurations, and will always cancel out.

....hope this helps...dac

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Received on Sat Dec 03 2005 - 04:53:01 PST
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