[gmx-users] Nonbonded energy Protein-Ligands

Steven Neumann s.neumann08 at gmail.com
Mon Oct 31 12:19:53 CET 2011

Dear Gmx Users,

My system consists of 10 ligands and protein. I am calculating the hydrogen
bonds between each residue and my ligands (LIG). The overall charge of each
ligand is zero.
I used:

g_hbond -f md2.trr -s md2.tpr -n SystemGRP.ndx -num

And I found one residue with avergae number of hydrogen bonds = 2.2 per
time frame which is quite a lot comparing to other residues.

Then I calculated the nonbonded energy between this residue and my 10

g_energy -f md2.edr -s topol.tpr -o 127LJwithLIG.xvg     - SR - LJ energy
res127-LIG = 0.659 kcal/mol

g_energy -f md2.edr -s topol.tpr -o 127CoulombWithLIG.xvg -SR - Coulomb
res127-LIG = -32.579 kcal/mol

The total energy (nonbonded) as a sum of LJ and Coulomb = -31.919 kcal/mol

My question is: how is it possible that contribution of Coulombic
attraction is so high if the overall charge of each ligand is zero? And why
the LJ potential seems to be slightly repulisve? Is the evidence of
hydrophobic attraction?

Thank you in advance,

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