We are currently running mmpbsa to calculate interaction energies between a
protein (223 amino acids) and a DNA fragment. Sander appears to give very
large eneriges for the bonded term. The trajectories were generated with
SHAKE constraints on all bonds involving hydrogens, while the internal
energies in mmpbsa is evaluated without SHAKE. Still it looks like
somethings is wrong with the bonded term. Does anyone have a clue? Any help
is gratefully appreciated!!
Here is part of the output:
MM
GB
PB
MS
1
BOND = 522344.8163 ANGLE = 2045.2765 DIHED = 2242.3395
VDWAALS = -1848.8571 EEL = -16237.6431 EGB = -2875.2331
1-4 VDW = 886.8738 1-4 EEL = 10209.1460 RESTRAINT = 0.0000
corrected reaction field energy: -4690.223908
surface area = 10453.803
Regards,
Magne Olufsen
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Magne Olufsen
Ph.D student
Work address
Department of Chemistry, Faculty of Science
University of Tromsų
9037 Tromsų, Norway
website
http://uit.no/115/3193/18?SubjectId=443&From=0
telephone +47 77644057
Fax: +47 77644737
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Received on Mon Dec 06 2004 - 13:53:00 PST
