Dear all,
I need to calculate binding energy calculation between a protein and a mof using gmx_MMPBSA. I have used Gromacs software to perform the following MD simulation steps: 1. I manually insert protein into the mof pore. 2. I performed energy minimization and simulated annealing by allowing the system to slowly change from 0 to 298 K. 3. I performed 10 ns NVT and NPT equilibration. Finally, I perform 10 ns MD production.
The force filed parameters for MOF is generated using OBGMX.
The problem is that I get a very large positive binding free energy (the experiment results show that this type of protein can enter into the MOF, so I expect a negative binding energy between the protein and the MOF). I would appreciate it if you could share your feedback with me so that I can improve the results. Furthermore, Gromacs MD analysis yields a positive LJ(SH) for the system; however, gmx_MMPBSA yields a negative value for the Van der Waals interaction. Could you please tell me why there is difference between these two parameters from Gromacs and gmx_MMPBSA?
Best regards,
Bahareh
Bahareh Bamdad
Assalam o alaikum wa rahmatullahi wa barkatuhu
I have shared a link for MMPBSA just follow the way
https://www.youtube.com/watch?v=EZK0Kql6QmA
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