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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