Dear amber users,
After allocating more memory, the entropy calculation works now (6000MB). But after review these results, I am not confident with them. In my system, I just did a single residue mutation, but I found very big entropy difference between different mutants. Here I showed part of the values below:
Wide: -8.39
D5A: -26.01
R7Q:-26.62
R7E:-5.9
W10A:-27.04
W10Y:-13.9
S4A:-34.44
R11A:-35.64
What I really want to say is,here, R11 is outside of the binding pocket. The mutational binding free energy excluded entropy is near to be 0. But here the entropy difference is more than 20! So may be there are some problem with my calculation?
(wide)
ENTROPY RESULTS (HARMONIC APPROXIMATION) CALCULATED WITH NMODE:
Wide:
Complex:
Entropy Term Average Std. Dev.
-----------------------------------------------------------
Translational: 17.4738 0.0000
Rotational: 18.4182 0.0000
Vibrational: 4937.7150 0.0000
Total: 4973.6070 0.0000
Receptor:
Entropy Term Average Std. Dev.
-----------------------------------------------------------
Translational: 17.4498 0.0000
Rotational: 18.3951 0.0000
Vibrational: 4794.9366 0.0000
Total: 4830.7812 0.0000
Ligand:
Entropy Term Average Std. Dev.
-----------------------------------------------------------
Translational: 14.2356 0.0000
Rotational: 12.7686 0.0000
Vibrational: 124.2156 0.0000
Total: 151.2198 0.0000
DELTA S total= -8.3940 +/- 0.0000
NOTE: All entropy results have units kcal/mol. (Temperature has already been multiplied in as 300. K)
(R11A)
ENTROPY RESULTS (HARMONIC APPROXIMATION) CALCULATED WITH NMODE:
Complex:
Entropy Term Average Std. Dev.
-----------------------------------------------------------
Translational: 17.4723 0.0000
Rotational: 18.4197 0.0000
Vibrational: 4907.4093 0.0000
Total: 4943.3013 0.0000
Receptor:
Entropy Term Average Std. Dev.
-----------------------------------------------------------
Translational: 17.4498 0.0000
Rotational: 18.3993 0.0000
Vibrational: 4801.8369 0.0000
Total: 4837.6860 0.0000
Ligand:
Entropy Term Average Std. Dev.
-----------------------------------------------------------
Translational: 14.1768 0.0000
Rotational: 12.6114 0.0000
Vibrational: 114.4686 0.0000
Total: 141.2571 0.0000
DELTA S total= -35.6418 +/- 0.0000
NOTE: All entropy results have units kcal/mol. (Temperature has already been multiplied in as 300. K)
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Very thanks for your help again!
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Received on Sat Jun 05 2010 - 19:30:03 PDT
