positive binding energy

[faryal....@gmail.com]

Dear g_mmpbsa users

I used the precompiler g_mmpbsa program to calculate the docked protein in complex to a peptide ligand.
I issued this command :

g_mmpbsa -f .xtc -s .tpr -n .ndx -i pbsa.mdp -pdie 2 -pbsa -decomp`

but obtained a summary_energy.dat file which displays:

van der Waal energy = -182.387 +/- 21.188 kJ/mol

Electrostattic energy = -730.898 +/- 69.629 kJ/mol

Polar solvation energy = 971.582 +/- 70.912 kJ/mol

SASA energy = -27.776 +/- 1.782 kJ/mol

SAV energy = 0.000 +/- 0.000 kJ/mol

WCA energy = 0.000 +/- 0.000 kJ/mol

Binding energy = 30.521 +/- 52.888 kJ/mol

I dont know how come the binding energy is positive?
I used gromos 54a7 force field
Is there anyone who can help me and tell me how come I got the binding energy + 30.521 kj/mol?

Thanks in advance
Farial

[g_mmpbsa Mailing List]

As wrote in in g_mmpbsa publication, we have tested MM/PBSA with Amber force field (all-atom force field). We cannot say validity of MM/PBSA with Gromos force field, which is a united atom force field. It does not contain non-polar hydrogen atoms and can drastically affect the surface computation during solvation energy calculation.

 Also, positive energy could come in docked complexes because some time ligand pose may not be favorable for binding after docking.