Dear all,
I calculated the entropy for a peptide+watershell system by using both
MMPBSA.py and MM_PBSA.pl.
Peptide+watershell :complex; peptide :ligand
Results for entropy that I got from these two scripts are different,
especially for the receptor (watershell) :
MMPBSA.py::
ENTROPY RESULTS (HARMONIC APPROXIMATION) CALCULATED WITH NMODE:
Complex:
Entropy Term Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
Translational 15.7572 0.0000
0.0000
Rotational 15.4116 0.0127
0.0073
Vibrational 1128.9861 13.2411
7.6448
Total 1160.1549 13.2525
7.6513
Receptor:
Entropy Term Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
Translational 13.7862 0.0000
0.0000
Rotational 14.2357 0.1439
0.0831
Vibrational 669.3464 47.3527
27.3391
Total 697.3683 47.2087
27.2559
Ligand:
Entropy Term Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
Translational 15.6553 0.0000
0.0000
Rotational 15.2580 0.0166
0.0096
Vibrational 732.7309 2.8869
1.6667
Total 763.6439 2.9028
1.6759
Differences (Complex - Receptor - Ligand):
Entropy Term Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
Translational -13.6842 0.0000
0.0000
Rotational -14.0821 0.1415
0.0817
Vibrational -273.0911 57.6574
33.2885
DELTA S total= -300.8573 57.5159
33.2068
MM_PBSA.pl::
# COMPLEX RECEPTOR
LIGAND
# ----------------------- -----------------------
-----------------------
# MEAN STD MEAN STD MEAN
STD
# ======================= =======================
=======================
TSTRA 15.85 0.00 13.87 0.00 15.75
0.00
TSROT 15.64 0.01 13.83 0.06 15.51
0.01
TSVIB 1017.93 14.25 323.39 18.15 757.42
2.50
TSTOT 1049.43 14.26 351.10 18.12 788.69
2.50
# DELTA
# -----------------------
# MEAN STD
# =======================
TSTRA -13.77 0.00
TSROT -13.70 0.05
TSVIB -62.88 25.46
TSTOT -90.35 25.42
As shown above, the number for the vibration part of entropy from the
Python script is twice as that from the perl script.
Has anyone compare the results from these two scripts before? Any comment
is welcome.
Thank you.
Nan
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 07 2012 - 12:00:04 PDT
