Positive Binding energy MMPBSA

[subhomoiBK]

GROMACS version:v.2018
Hi,

I have simulated multiple systems (dimer+ligand) for 200 ns and trying to calculate the MMPBSA binding energy using g_mmpbsa. However, I am getting positive binding energy in each case. The ligand is occupying the dimer interface throughout the simulation. I have used multiple snapshots as well, but the issue remains the same. Kindly suggest some solutions.

van der Waal energy = -174.342 +/- 1.326 kJ/mol

Electrostattic energy = -240.423 +/- 1.615 kJ/mol

Polar solvation energy = 458.646 +/- 2.744 kJ/mol

SASA energy = -23.333 +/- 0.079 kJ/mol

Binding energy = 20.462 +/- 1.507 kJ/mol

Thanks,

S Borkotoky

[jdandrade]

Hi @subhomoiBK.

As I explained in the topic below:

MM/PBSA for the latest gromacs versions

Hi @ncheron . As I mentioned, my protocol only works with MMGBSA (All my three different attempts failed for MMPBSA). Also, it seems to need a fully compiled ambertools (no errors). Given that: A: Gromacs Files Preparation: load the environment variables from both gromacs and ambertools: source …/bin/GMXRC test -f …/ambertools/amber.csh && source …/ambertools/amber.csh Set a few variables for work: set JUMP = 10 set TOP = full_system_topology_file.top set CTOP = dessolvated_system_…

I was unable to succeed in my MMPBSA calculations with g_mmpbsa (pretty much se same issue), but I was successful with MMGBSA within ambertools.

I would suggest you to take a look at the instructions I provided and give it a try.

Best regards, take care.