AMBER Archive (2004)

Subject: Re: AMBER: build a cyclic peptide

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Nov 24 2004 - 15:56:44 CST

>Yes, the bond is still long and energy is still high
>(~100kcal/mol) even after 5000 NCYC.

This is why the minimizer in xleap is so much better
for cleaning up things - faster, and visual so you can
fix the good parts and relax the others.

Note that it doesn't take nonbonded terms into account,
so overlaps need manual attention.

Bill
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