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-- Ray Luo, Ph.D. Professor, Biochemistry, Molecular Biophysics, and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Mon, Jun 2, 2014 at 1:48 PM, Lara rajam <lara.4884.gmail.com> wrote: > 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 > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Jun 02 2014 - 16:00:02 PDT