On Tue, Sep 21, 2010, Baptiste Legrand wrote:
> So, the positive total energy (~ 5.0 10+1) observe after the
> minimization could be related to the wrong parametrization of the gaff
> forcefield for this type of molecule? (with non classical peptidic bond
> but CO-NH-NH-C (side chain)-CO-NH-NH-...). Thanks
Why do you think a positive energy is "bad"? The zero of energy is arbitrary.
You should see if minimization moves the structure away from a "good" starting
point by too large an amount.
....dac
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Received on Tue Sep 21 2010 - 09:00:16 PDT
