[gmx-users] g_mmpbsa positive binding energy

tasneem kausar tasneemkausar12 at gmail.com
Fri Oct 23 10:02:55 CEST 2015

Dear Gromacs Users
I am trying to calculate binding energy of protein-ligand and
protein-receptor complex using g_mmpbsa. I have run simulation of 10 ns and
snapshot was generated at every 1 ps. Initial 2ns was not taken. g_mmpbsa
was run for the rest of the frames. The command line was given as:
g_mmpbsa -f protein.xtc -s protein.tpr -n protein.ndx -dt 200 -b 2000 -e
10000 -pdie 2
protein.ndx is index file of protein-ligand and protein-receptor.
 The binding energy with dielectric 2 comes out positive.  When I have
increased the dielectric, binding energy is still positive.
at dielectric 2  binding energy was 1028.010 kJ/mole
at dielectric 4  binding energy was 428.010 kJ/mole
at dielectric 8  binding energy was 128.015 kJ/mole
I have calculated the charge on the ligand and receptor using pdb2gmx. The
charge on the ligand protein is -12 and that of receptor protein is -5.
 How will I get the negative binding energy?
Any suggestion resolving this issue will be appreciated.

Thanks in Advance

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