[gmx-users] Nonbonded energy Protein-Ligands

[Steven Neumann]

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
RESIDUEwithLigandsHbond.xvg

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
ligands:

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,



Steven
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