[gmx-users] Nonbonded energy Protein-Ligands
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.
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
Thank you in advance,
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