AMBER: Neutralize charges for simulated annealing?

From: Francesco Pietra <>
Date: Sat, 11 Aug 2007 15:35:30 -0700 (PDT)

I have built the pdf file for a very large (> 3000 Da) non polymeric molecule,
bearing two sulfate esters group, thus two negative charges.

Should antechamber succeed, I intend to carry out simulated annealing in vacuum
to sample conformations in view of MD in explicit solvents. To this end is it
advisable to neutralize the charges with two sodium atoms before the in vacuum
sim annealing? If so, is xleap + prepin + addion OK?

francesco pietra

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Received on Sun Aug 12 2007 - 06:08:11 PDT
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