AMBER Archive (2005)

Subject: AMBER: Creating an Ester with Antechamber/Gaff

From: John O'Mahony (john.omahony_at_gmail.com)
Date: Thu Dec 01 2005 - 03:46:40 CST

Dear all,

 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??

Thanks

John


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