Date: Tue, 3 Mar 2015 09:33:51 +0800
Dear All,
I am doing simulation on system that with various compounds bonded to the
N-terminal of certain peptide, like shown in the following picture. Now I
am facing the problems with creating unit for such N-Cap residue.
1. Should I treat R1 combined R' as a N-Cap residue or just the R' only?
2. In any case above, is there any method available to assign correct
partial charge and atom type for such non-standard residue?
Thanks a lot for your suggestions in advance!
Best Regards,
Tao
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
(image/png attachment: nonstand_cap_residue.png)
