Hi Tommaso,
I've investigated phosphate ions a little, but haven't done a thorough
investigation. I can tell you that the only way I could get the Na+ and
phosphate ions not to aggregate was to use OPC water and increase the
phosphate oxygen parameters similar to what Steinbrecher et al. propose for
bioorganic phosphates.
http://pubs.acs.org/doi/abs/10.1021/ct300613v
But this is more of a starting point for further investigation than a
recommended solution.
Best,
--Niel
On Thu, Sep 8, 2016 at 1:49 AM, Casalini Tommaso <
tommaso.casalini.chem.ethz.ch> wrote:
> 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 - 19:30:02 PDT
