I'm having problems charge getting the parameters for a CY3 dye, I initially
used antechamber, but then discovered antechamber couldn't be used if you were
working with a molecule fragment.
as the CY3 dye is going to be attached to a strand of RNA, I discovered the
program RED is supposed to be capable of getting the parameters.
however I'm having trouble choosing a cap for the unbonded oxygen on the CY3
dye, I was thinking that a suitable cap would be a PO4 group however I'm not
sure what the charge should be constrained to.
any tips?
-James Moore
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Received on Wed May 20 2009 - 12:26:00 PDT
