[gmx-users] Force field selection for free Bicarbonate molecules in solution
Vitaly V. Chaban
vvchaban at gmail.com
Fri Sep 4 17:22:02 CEST 2015
My group works with the bicarbonate and similar anions in the context
of CO2 chemisorption.
You must exercise serious caution to assign correct electrostatic
potential at the surface of the anion and account for
hydration/solvation effects within the force field derivation
On Fri, Sep 4, 2015 at 8:42 AM, Faulkner, Matthew
<M.Faulkner at liverpool.ac.uk> wrote:
> I am trying to find a suitable force field for using Bicarbonate in an aqueous environment in my MDS. I can't find anything where Bicarbonate has been used this way in gromacs in the literature, does anybody know of a reference for me or have advice on which force filed would be best?
> I have run several MDS in the OPLS-AA force field for my protein of interest in solution with water and various ions and they work very well,but I would like to add 150 mM HCO3- into my environment. I have a PDB and TOP file prepared using PRODRG for the HCO3- but I'm not sure if the OPLS-AA force field is suitable for this molecule.
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