[gmx-users] Nonbonded energy Protein-Ligands

Mark Abraham Mark.Abraham at anu.edu.au
Mon Oct 31 12:54:11 CET 2011

On 31/10/2011 10:19 PM, Steven Neumann wrote:
> 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?

Consider two neutral dipoles fixed either parallel or anti-parallel to 
each other.

> And why the LJ potential seems to be slightly repulisve? Is the 
> evidence of hydrophobic attraction?

First, define "hydrophobic attraction" :-)

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