Dear all,

I have been trying to calculate MMPBSA free energy. I have followed the procedure describe in http://rashmikumari.github.io/g_mmpbsa/. However, I am confused with too large value of binding energy and solvation energy. I have pasted the results for your kind perusal. The protein have approximately 8000 atoms and drug consists of 40 to 60 atoms. For your information, I am using the pre-compiled version of the g_mmpbsa with gromacs-4.5.5.

Polar Solvation energy::

Time Protein PB energy DRUG PB energy TOTAL

0.000 -6036.543 -32.379 -6034.673

100.000 -8261.230 -31.227 -8248.527

200.000 -8348.989 -31.381 -8340.070

300.000 -8266.191 -32.000 -8253.746

400.000 -8768.965 -32.329 -8755.099

500.000 -8941.207 -32.271 -8928.928

600.000 -9180.776 -30.941 -9169.837

700.000 -9059.171 -31.609 -9036.116

800.000 -9107.771 -30.959 -9097.935

900.000 -8686.404 -31.295 -8667.624

1000.000 -8348.161 -32.097 -8334.050

Polar Solvation energy with SASA model::

Time Protein-Surf-ten energy DRG-Surf-ten energy Total

0.000 522.350 11.246 516.566

100.000 555.009 11.561 549.391

200.000 556.254 13.772 551.694

300.000 537.388 13.863 533.235

400.000 554.905 13.744 551.202

500.000 540.928 12.385 537.020

600.000 534.929 13.370 529.182

700.000 545.511 13.535 541.450

800.000 534.283 12.854 530.786

900.000 532.137 12.763 527.951

1000.000 530.363 13.407 526.851

All the the energy values are given in kJ/mol....

Thanks in Advance,

Kalyanashis Jana