[AMBER] Problem with Creating Unit for Non-standard N-Cap Residue

From: Huang Tao <thuangsh.gmail.com>
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,

AMBER mailing list

(image/png attachment: nonstand_cap_residue.png)

Received on Mon Mar 02 2015 - 18:00:04 PST
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