Hello to everyone,
I'm experiencing some problems in an MM-PBSA calculation. My system
consists of enzyme, cofactor (NADPH) and inhibitor. Previous
calculations (on different enzyme conformers) run fine, while for this
specific case the final delta PBTOT I obtained is way to large
(-324.94), mostly due to an imbalanced delta GAS (-356.32; in particular
my delta INT is -120.87 and delta VdW is -216.83). The topology files
and the crd of complex, receptor and ligand look nice when I visualize
them in VMD), no bonds are distorted or broken, etc.
Hereafter my output file of the MM-PBSA calculation:
# COMPLEX RECEPTOR
LIGAND # ----------------------- -----------------------
-----------------------
# MEAN STD MEAN STD
MEAN STD
# ======================= =======================
=======================
ELE -7236.85 96.82 -7192.48 96.10
-25.76 0.48
VDW -1199.12 28.96 -993.70 30.53
11.41 1.22
INT 5792.37 46.59 5882.25 51.16
30.99 3.65
GAS -2643.60 103.44 -2303.93 106.04
16.64 3.53
PBSUR 104.29 1.24 105.77 1.26
3.44 0.02
PBCAL -3415.05 88.12 -3424.16 88.17
-27.19 0.51
PBSOL -3310.76 87.43 -3318.39 87.45
-23.75 0.51
PBELE -10651.91 32.14 -10616.63 32.91
-52.95 0.58
PBTOT -5954.37 44.68 -5622.32 51.50
-7.11 3.48
# DELTA # -----------------------
# MEAN STD
# =======================
ELE -18.62 6.32
VDW -216.83 5.70
INT -120.87 16.97
GAS -356.32 17.62
PBSUR -4.92 0.17
PBCAL 36.30 4.20
PBSOL 31.38 4.23
PBELE 17.68 5.12
PBTOT -324.94 17.04
What can the reason for such huge energy differences be? Where should I
search for the mistake (If any is in)?
Attached you can find input, output for the mm-pbsa calculation, as well
as prmtop and crd of ligand, "receptor (protein and cofactor)" and complex.
Many thanks,
Matthias Negri
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Received on Wed May 05 2010 - 03:30:03 PDT
