Dear Amber
I tried to calculate the binding energy for a protein complex with
MMPBSA.
I followed the tutorial page "
http://ambermd.org/tutorials/advanced/tutorial3/section3.htm"
and used the perl script .
On running the script extract_coords.mmpbsa the snapshots are created and I
used the corresponding prmtop files for my complex protein and ligand like
the tutorial.
I used the binding_energy.mmpbsa for the energy calculation.
it first gave a error in linking the library path and i have fixed it by
sourcing
setenv LD_LIBRARY_PATH /user/AMBERHOME/amber14/lib, after that the there
is no error
but when i run the binding_energy.mmpbsa
the error is as follows regarding to the frames 1, 2 and 3
1
BOND = 377.7873 ANGLE = 971.0699 DIHED =
1292.2246
VDWAALS = -1027.3149 EEL = -8162.5125 EGB =
-2189.5589
1-4 VDW = 456.0451 1-4 EEL = 3910.6949 RESTRAINT =
0.0000
corrected reaction field energy: -3478.997510
2
BOND = ************* ANGLE = 234201.6394 DIHED =
6718.6100
VDWAALS = ************* EEL = 991.5371 EGB =
-24632.2619
1-4 VDW = 2579060.1202 1-4 EEL = -452.1629 RESTRAINT =
0.0000
corrected reaction field energy: -36971.914155
3
BOND = ************* ANGLE = 240012.6743 DIHED =
6831.4244
VDWAALS = ************* EEL = -437.7225 EGB =
-23129.0534
1-4 VDW = 2317884.7200 1-4 EEL = -271.8009 RESTRAINT =
0.0000
corrected reaction field energy: -34613.804911
I am not understanding what could be wrong , can any one let me know where
i need more understanding to solve this
thank you
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Received on Mon Jun 02 2014 - 14:00:02 PDT
