Binding energy

[helios thorfin]

Dear All,

I have conducted gmx_mmpbsa calculations utilizing the CHARMM 36 force field for protein-ligand interactions. Over the last 10 nanoseconds, the binding energy has stabilized at approximately -6. Based on insights gained from previous inquiries, it has been recommended to adjust certain parameters for the Generalized Born (GB) calculation to enhance the accuracy and precision of the binding energy values.

I came across a valuable resource, the website: https://casea1998.cn/2022/04/17/gmx-MMPBSA/, which comprehensively outlines the parameters involved in the Poisson-Boltzmann calculation. My specific inquiry pertains to identifying the critical parameters that, through slight adjustments, can lead to improved binding energy values.

[marioe911116]

The introduction (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/introduction/), input file page (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/input_file/) and this publication (https://pubs.acs.org/doi/10.1021/acs.jpcb.2c07079) could give something to start with