Dear Amber users and developers,
I would like to simulate phosphate ions in water solution (hydrogen phosphate and dihydrogen phosphate) in order to reproduce PBS environment for siRNA characterization.
For this purpose, I obtained atomic charges through RESP formalism (ESP computed at HF/6-31G* level of theory).
I used atom types and parameters taken from leaprc.phosaa10 and frcmod.phosaa10.
I would like to know if such parameters are suitable for the simulations of those ions (I can imagine that polarization effects can play a role).
I also observed ions clustering, and I think it can be an artifact. I tried to look for articles concerning this problem, but I was not able to find something useful.
Have you some suggestions?
Thanks a lot in advance,
Tommaso
Tommaso Casalini, PhD
Post Doctoral Fellow
ETH Zurich
Institute for Chemical- and Bioengineering
Morbidelli Group, HCI F137
Vladimir-Prelog-Weg 1
8093 Zurich, Switzerland
tommaso.casalini.chem.ethz.ch<mailto:tommaso.casalini.chem.ethz.ch>
Phone: +41 (0)44 632 61 83
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Received on Thu Sep 08 2016 - 02:00:03 PDT
