Hi, all
I use the script of MMPBSA.py and mm_pbsa.pl respectively to
calculate the entropy contribution of the same frames, but the results
were quite different! The result of quasi-harmonic:
ENTROPY RESULTS (QUASI-HARMONIC APPROXIMATION) CALCULATED WITH PTRAJ:
Translational Rotational Vibrational
Total
Complex: 17.0124 17.6648 683.8306
718.5078
Receptor: 16.9934 17.6532 681.4254
716.0719
Ligand: 13.5885 11.9472 95.7974
121.3333
DELTA S: -13.5694 -11.9355 -93.3922
-118.8974
The value is as large as -118.8974 kcal/mol!
The result of normal mode using mm_pbsa.pl script is:
# DELTA
# -----------------------
# MEAN STD
# =======================
TSTRA -13.65 0.00
TSROT -12.03 0.03
TSVIB -1.64 7.36
TSTOT -27.32 7.36
Their translational and rotational entropy values are close, but their
vibrational entropy values are quite different! The input file of
quasi-harmonic calculation is:
|&general
| startframe=2000, endframe=5000, interval=10,
| verbose =2,
| entropy =1,
| strip_mask=:WAT:Cl-
|/
So why the vibrational entropy contribution from quasi-harmonic and
normal mode methods are so different?
I would be appreciate for the helps!
Liu Wei
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Received on Wed Jul 01 2015 - 02:30:02 PDT
