A brief minimization could fix the bond length. You could limit local distortions by selecting the atoms to minimize in xleap and minimizing there. Note leap does not use vdw when minimizing, so watch for steric issues when doing this.
Or you could just see if equilibration fixes it without too much distortion.
Bill
<div>-------- Original message --------</div><div>From: George Tzotzos <gtzotzos.me.com> </div><div>Date:03/20/2015 10:55 AM (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject: [AMBER] Leap warning </div><div>
</div>I’m setting up new topology files and Leap throws the warning below.
Is there a way to fix the bond length? Or should the warning be ignored?
Thanks for any suggestions
George
Checking Unit.
WARNING: There is a bond of 3.727786 angstroms between:
------- .R<CYX 104>.A<SG 8> and .R<CYX 53>.A<SG 8>
-- ignoring the warning.
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Received on Fri Mar 20 2015 - 11:30:11 PDT
