AMBER Archive (2009)

Subject: [AMBER] How to build amide bond etween two protein chains

From: journal.update (journal.update_at_gmail.com)
Date: Tue Jun 23 2009 - 23:36:07 CDT

Dear amber users,

  I have modified protein system that need construct top and crd files in xleap. Sidechain (NH2) of non-terminal Lysine in protein A form amide with C-terminal (C=O) of protein B, the whole system seems like fork or "Y" sharp. In leap, I have tried to directly build bond between N atom of Lysine in protein A and C atom in protein B, but hydrogen can not match request. How can deal with such situation? Built new residue type or any other ideas? Thanks a lot.

Jian
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