Positive Binding energy MMPBSA

[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.