> Well, I thought that a positive energy was unfavorable and means that my
> initial structure was really "bad" (bad angles, steric clashs etc...).
> These are the first and the last step of the minimization, it doesn't
> seem to be bad. The energy decrease from 2.3221E+02 to 3.9699E+01. I
> will read the chapter about the energies in the amber manual.
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 2.3221E+02 3.1148E+01 1.5869E+02 C2 56
>
> BOND = 54.0796 ANGLE = 82.7820 DIHED =
> 78.4045
> VDWAALS = -4.4471 EEL = -96.1161 HBOND =
> 0.0000
> 1-4 VDW = 24.8639 1-4 EEL = 92.6435 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 52000 3.9699E+01 3.2797E-04 1.3263E-03 C5 38
>
> BOND = 2.8199 ANGLE = 11.0717 DIHED =
> 30.4281
> VDWAALS = -12.5402 EEL = -113.4219 HBOND =
> 0.0000
> 1-4 VDW = 20.0602 1-4 EEL = 101.2809 RESTRAINT =
> 0.0000
This looks good. The energy decreased and the RMS and maximum value of the gradient is close to zero in the final structure with means you are at a minimum.
All the best,
Andy
--
Dr. Andreas W. Goetz
San Diego Supercomputer Center
Tel : +1-858-822-4771
Email: agoetz.sdsc.edu
Web : www.awgoetz.de
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Received on Wed Sep 22 2010 - 10:00:05 PDT
