Hi.
I performed MMpbsa analysis for a protein protein complex with 424 and 248 residues for each protomer in the presence solvent. The trajectory length was 10ns. Dielectric constant was 2 and solvent dielectric was set to 75. The result was vague. The binding energy was almost +900 kj/mol.
g_mmpbsa -f xtc -s tpr -n ndx -i pbsa.mdp -pdie 2 -pbsa -decomp`
group chosen :13 and 14 [ Chain A and chain B respectively]
Do I do anything wrong?
vdw = -578
electrostatic = +1252
polar solvation = +381
sasa energy = -71
binding energy = +983
Hi,
Try increasing the dielectric constant (pdie) in the command line as well as the mdp files. Increase the pdie to 4, default value being 2.
HI Rahul Suresh,
May I ask if it is possible to calculate entropic contribution for such large complex?
- Badges
- Science topic