# mm_pbsa and statistic program

From: Pascal Bonnet <pascal.bonnet_at_man.ac.uk>
Date: Thu 26 Sep 2002 11:50:52 +0100

Hi,

1) From the /amber6/src/mm_pbsa/EXAMPLE1 directory I run the
mm_pbsa_statistic and mm_pbsa_statistic_independent programs and I
obtain same values for the average energies but different values for the
standard deviation (STD).

Why is there a difference for STD?

2) Also, having the average energies and the STD of the complex (AB),
ligand (B) and the receptor (A), is it possible to calculate the STD of
the interaction [AB-(A+B)] ? In fact, is it possible to verify the STD
interaction values using only the output file statistics.out? I don't
think so.

Pascal

output files (statistics.out):
using the mm_pbsa_statistics program
----------------------------------------------------------------------------------
Complex (AB) Receptor (A)
Ligand (B)
Contribution ----------------------- ----------------------
----------------------
mean std mean std
mean std
----------------------------------------------------------------------------------
Eelectrostat -2938.8112 30.6149 -2551.3708 25.0410
-254.9764 9.3279
EvdW -395.9564 15.4541 -325.0707 12.6982
-15.1583 5.1366
Einternal 1679.6075 27.4865 1463.1858 25.7948
216.4217 12.2377
Egas -1655.1601 37.4513 -1413.2557 32.4162
-53.7130 10.8955
E(nonpolar) 34.1723 0.9605 31.6138 0.2951
10.2315 0.1214
E(nonpolGB) 44.1728 1.2759 40.7740 0.3920
12.3696 0.1613
E(GB) -1180.0048 31.1711 -1116.6541 21.7505
-210.0049 7.0357
E(solvation) -1135.8320 31.1002 -1075.8801 21.5896
-197.6353 6.9136
E(GB+elect) -4118.8160 11.2174 -3668.0249 12.3156
-464.9813 5.2531
E(total,GB) -2790.9921 16.9781 -2489.1358 18.3113
-251.3484 9.5759
----------------------------------------------------------------------------------
Interactions [AB-(A+B)]
------------------------------------
Contribution mean std
------------------------------------
Eelectrostat -132.4640 12.9279
EvdW -55.7274 2.5744
Egas -188.1914 13.3941
E(nonpolar) -7.6730 0.8560
E(nonpolGB) -8.9707 1.1371
E(GB) 146.6542 12.1611
E(solvation) 137.6835 12.1024
E(GB+elect) 14.1902 2.3702
E(total,GB) -50.5079 2.7140

using the mm_pbsa_statistics_independent program
----------------------------------------------------------------------------------
Complex (AB) Receptor (A)
Ligand (B)
Contribution ----------------------- ----------------------
----------------------
mean std mean std
mean std
----------------------------------------------------------------------------------
Eelectrostat -2938.8112 30.6149 -2551.3708 25.0410
-254.9764 9.3279
EvdW -395.9564 15.4541 -325.0707 12.6982
-15.1583 5.1366
Einternal 1679.6075 27.4865 1463.1858 25.7948
216.4217 12.2377
Egas -1655.1601 37.4513 -1413.2557 32.4162
-53.7130 10.8955
E(nonpolar) 34.1723 0.9605 31.6138 0.2951
10.2315 0.1214
E(nonpolGB) 44.1728 1.2759 40.7740 0.3920
12.3696 0.1613
E(GB) -1180.0048 31.1711 -1116.6541 21.7505
-210.0049 7.0357
E(solvation) -1135.8320 31.1002 -1075.8801 21.5896
-197.6353 6.9136
E(GB+elect) -4118.8160 11.2174 -3668.0249 12.3156
-464.9813 5.2531
E(total,GB) -2790.9921 16.9781 -2489.1358 18.3113
-251.3484 9.5759
----------------------------------------------------------------------------------
Interactions [AB-(A+B)]
------------------------------------
Contribution mean std
------------------------------------
Eelectrostat -132.4640 40.6366
EvdW -55.7274 20.6509
Egas -188.1914 50.7161
E(nonpolar) -7.6730 1.0121
E(nonpolGB) -8.9707 1.3445
E(GB) 146.6542 38.6551
E(solvation) 137.6835 38.4854
E(GB+elect) 14.1902 17.4671
E(total,GB) -50.5079 26.7443
------------------------------------
Received on Thu Sep 26 2002 - 03:50:52 PDT
Custom Search