AMBER Archive (2009)

Subject: [AMBER] CY3 dye parameters

From: jcmoore_at_student.umass.edu
Date: Thu Apr 23 2009 - 16:42:59 CDT


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

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber