AMBER Archive (2009)

Subject: [AMBER] problem of mm_pbsa

From: Qinghua Liao (fantasticqhl_at_yahoo.com)
Date: Wed Aug 05 2009 - 00:46:51 CDT

Hi amber users,
I have a problem when I use mm_pbsa in amber 10 to calculate the binding energy of the complex. After docking using autodock 4.0, I chose a conformation of the ligand, which matched well with the crystal ligand in the complex, to do MD with the receptor, two structural waters were preserved. I got a sample of 4ns, a equilibrated system according to the RMSD of the backbone.

But the binding energy is abnormal:

#                  COMPLEX                RECEPTOR                  LIGAND       
#          ----------------------- ----------------------- -----------------------
#                  MEAN        STD         MEAN        STD         MEAN        STD
#          ======================= ======================= =======================
ELE            -8427.58     249.82     -7913.17     248.20      -504.26      14.77
VDW         21573827.80   32502.03  20373193.05   31945..80   1200511.78    3894.24
INT          7034641.54   60631.76   6982919.11   60080.98     51722.43    5624.52
GAS         28600041.76   67739.75  27348198.98   66677.44   1251729.96    7136.00
PBSUR            104.47       1.36       104.04       1.33         4.94       0.08
PBCAL          -6167.49     140.62     -6144.17     142.81      -128.34      10.10
PBSOL          -6063.02     140.19     -6040.13     142.34      -123.40      10.08
PBELE         -14595.07     231.58    -14057.35     225.77      -632.60      14.24
PBTOT       28593978.74   67733.12  27342158.85   66668.31   1251606.56    7134.74
GBSUR            104.47       1.36       104.04       1.33         4.94       0.08
GB             -7508.97     158.41     -7502.67     156.03      -108.80       8.85
GBSOL          -7404.50     158.03     -7398.62     155.70      -103.86       8.83
GBELE         -15936.55     195.91    -15415.84     191.87      -613.06      13.92
GBTOT       28592637.26   67731.79  27340800.36   66668.02   1251626.10    7134.65
#                    DELTA       
#          -----------------------
#                  MEAN        STD
#          =======================
ELE              -10.15      18.22
VDW              122.97     158.98
INT                0.00       0.00
GAS              112.82     163.49
PBSUR             -4.51       0.32
PBCAL            105.02      23.41
PBSOL            100.51      23.25
PBELE             94.88      17.49
PBTOT            213.33     157.50
GBSUR             -4.51       0.32
GB               102.50      16.59
GBSOL             97.99      16.44
GBELE             92.35      11.01
GBTOT            210.81     159.42

The running of mm_pbsa is successful without any abnormal situation. What is the problem? And how can I figure it out? Any response will be highly appreciated!

All the best,

Qinghua Liao

      
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