Dear Amber developers and users,
I want to modify the Amber force field for nucleotides with modification in
the ribose ring. I would like to save all partial charges for nucleobases
and phosphates and change them only for ribose. But if I calculate charges
(using antechamber) for the entire nucleotide, all charges would be
modified (including charges on the nucleobases).
If I calculate charges for the ribose ring only (assuming it is neutral)
and then add them to charges for the rest of the nucleotide, the total sum
of charges on phosphate + nucleobases + ribose will not be =-1 anymore.
How can I update charges for the ribose only, without changing charges on
nucleobase and phosphate, and at the same time keep total charge = -1?
Maybe there is a way in antechamber to constrain charge on certain atoms
during calculation of charges? Is there a special option (special flag?)
for that?
Thank you,
Farkhad
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Received on Thu Oct 01 2020 - 18:30:02 PDT
