New partial charges after patching

From: Sadegh Faramarzi Ganjabad (
Date: Sat Jun 14 2014 - 04:15:47 CDT


I have connected side chain of ASP residue to side chain of LYS by a patch
to get a cyclic peptide; an oxygen atom of ASP side chain and two hydrogen
atom of LYS are deleted and the resulting patch is

1HB1 1HB2
   \ /
         2NZ- 2HZ1
  2HE2 - 2CE- 2HE1

However, I'm wondering how should I assign atomic partial charges to this
part of molecule. ASP was negatively charged before patch to LYS which was
positively charged. Do you have any idea about how to update partial
charges after patch?

Thanks in advance

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