GROMACS version: 2023.3
GROMACS modification: Yes/No
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Hi to all,
I am completed MD Simulation for protein_ligand complex. After proceed for MMPBSA analysis using gmx_MMPBSA method and In this results delta total energy is 551.03 . Can you explain why delta total energy is positive and high? How to solve this issue?
Am attaching the MMPBSA file.
FINAL_RESULTS_MMPBSA (2).dat (7.6 KB)
ligand is bound to the receptor? we dont know without knowing the details of the simulation and your set up. A postive energy in general indicates repulsive/ unfavourable- the reasons can be many, bad paramtes, bad set up and unfavourable ligand molecule etc.
Thank you for your response @scinikhil. First I do docking with protein and ligand, the result of binding score is -10.73. An observe the amino acids of protein is attached to the ligand and after am moving to the MD Simulations using gromacs and am run the simulation for 100ns with CHARMM36 force field and TIP3 water model. Here am attached to the results in of RMSD, RMSF, Rg, SASA and Hbonds.
Can you please help me to find out why MMPBSA value is high positive and how to correct this issue?
check the trajectory and make sure ligand is at the binding pocket, if it is there it is issue with your mmpbsa set up.
Thankyou for your reply @scinikhil. Using the VMD am visualize the trajectory file and The ligand is at the receptor active site. I run MMPBSA for 6 complexes and In 5 complexes MMPBSA value is negative like -23, -16, 19, -7 and -24 but one complex is getting 523 in this the VWD and GAS phase is getting positive values.
Can you tell me how to solve this problem?
