[AMBER] maximum simulated annealing temperature in explicit solvent

From: Thomas Evangelidis <tevang3.gmail.com>
Date: Thu, 21 Nov 2013 12:23:25 +0200

Dear list,

What is the maximum temperature one could use in a simulated annealing
protocol with an explicit solvent model (e.g. SPC/E)? I have a peptide with
a lot of NOE restraints and J-couplings and I would like to create native
like conformations. The reason I prefer the explicit solvation is because I
had bad experience with implicit solvent simulations of intrinsically
disordered peptides. I had initiated a relevant thread in the past where I
stated that at the end all the peptides adopted a helical conformation
which was in disagreement with the NMR and CD spectra.


Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens
email: tevang.pharm.uoa.gr
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Thu Nov 21 2013 - 02:30:03 PST
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