On Fri, Feb 07, 2025, Gabriel Ernesto Jara via AMBER wrote:
>
>I want to parametrize the HPO4²⁻ ion. The ion is bound to a polarizing
>active site.
The paper you reference is this one (included for other on the list, since
I had trouble finding it on the link you provided):
%A T. Steinbrecher
%A J. Latzer
%A D.A. Case
%T Revised AMBER Parameters for Bioorganic Phosphates
%J J. Chem. Theory Comput.
%V 8
%P 4405-4412
%D 2012
>or due to be highly charged, is better to calculate the RESP charges?
These phosphate calcualations used RESP charges for the simplest phosphates,
so those charges are the ones that are compatible with the LJ parameters
discussed in the paper. RESP charges are far from perfect, but are likely
to be better than am1bcc or abchg2 for this sort of ion.
...hope this helps...dac
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Received on Mon Feb 10 2025 - 07:30:02 PST
