On Fri, Nov 25, 2011, kanika sharma wrote:
>
> I ran tleap on a monomeric protein 1CSQ followed by sander for energy
> minimization with distant dependent dielectic constant. The parameters are:
>
>
> In the end when i studied the output file for the last cycle energy it is:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2000 1.8255E+02 1.3963E-01 1.0133E+00 CE2 133
>
> BOND = 17.3608 ANGLE = 79.8825 DIHED = 505.6139
> VDWAALS = -508.3373 EEL = -413.0355 HBOND = 0.0000
> 1-4 VDW = 211.1170 1-4 EEL = 289.9485 RESTRAINT = 0.0000
>
> I donot understant ehy the energy is so high? this happens with almost all
> the crstal structures that i use.
These look like standard energies to me. The absolute value of a molecular
mechanics energy function is pretty arbitrary, and only relative values of
the energy for different conformations has a good physical meaning.
....dac
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Received on Fri Nov 25 2011 - 05:30:03 PST
