AMBER Archive (2004)

Subject: Re: AMBER: build a cyclic peptide

From: Bill Ross (
Date: Wed Nov 24 2004 - 12:39:15 CST

> I did build the top and crd files with a long bond
> between two ends by using "bond" command. However, the
> minimization does not result in a reasonable
> structure.

I would try drawing the bond in xleap, minimize there, and
clean up manually by dragging atoms & reminimizing selected

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