[AMBER] Assigning protonation o residues for parallel tempering

From: Francesco Pietra <chiendarret.gmail.com>
Date: Tue, 9 Jul 2013 19:04:58 +0200

I am preparing files for parallel tempering to hopefully get a
dominant cluster of conformations for the unstructure (X-ray diffr)
tails of a protein homotrimer.

A problem: Poissson-Boltzmann calculations of pKa assign diprotonation
to most histidines of these tails (generated with MODELLER), except
for one subunit, where one histidine is assigned HIE. The apparent
reason is that this particular histidine comes closer (according to
MODELLER) to two other tails, while the other histidines of these
tails feel the bulk solvent. There is no reason that this represents a
low-energy situation.

I expect that parallel tempering is biased by the protonation assigned
to any titrable group for cases as illustrated above.

Grateful for advice.

francesco pietra

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Received on Tue Jul 09 2013 - 10:30:02 PDT
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