[MMTK] Energy calculations

Shirley Hui shirleyhui at alumni.uwaterloo.ca
Fri May 14 17:38:28 CEST 2004

I ran some tests to calculate the energies for different proteins.  I
noticed that in general, the energy values I get back from MMTK, are usually
extremely negative compared to energy values I get from other applications.
For example, I have compared the energies obtained from MMTK (amber 94) to
applications like MOE and TINKER (charmm27).  A summary of the results is

PDB Code    MOE        TINKER            MMTK
1cam.pdb ... 1049.900 ... -10.2100 ... -18735.6741
1cdn.pdb ... 503.588 ... 473.0359 ...       failed
1cbd.pdb ... 93000004 ... 1371.3984 ... failed
1ccm.pdb ... 372.207 ... 129.8959 ... 8035.69895
1top.pdb ... 3690.704 ... 3988.6323 ... 13780.5886
2bbm.pdb ... 3649.224 ... 5618.9214 ... failed

Does anyone know why the values are so large or so negative?
I realize that different applications will calculate energies differently.
Is is just a matter of the fact that the implementations for calculating
energies is different though?  Does it depend on the parameter files used as
well (i.e. charmm27 vs amber94) To me there seems be a VERY large
discrepancy??  At least between TINKER and MOE the different is not AS huge.
OR is it that my MMTK is not working properly?  I was wondering if anyone
could confirm my MMTK results??  The pdbs were all obtained from the protein

thanks for any insight,

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