Hello everyone, i hope you all are doing well,
I have performed docking study with some selected molecules along with the reference inhibitor and the docking results were for selected two compound for MD analysis were -9.5 kcal and -8.9 kcal, while the reference inhibitor showed -9.7 kcal/mol binding energy. After that MD simulation were performed via GROMACS and proposed drug portray more promising results than the reference inhibitor, but with the same trajectory when i am doing MMGBSA analysis via gmx_MMPSA, it shwed total delta score -8.656 and -10.56 kcal/mol. while the MMGBSA result for reference inhibtor were -19.6 kcal/mol.
Kindly let know me some reson behind the same and is it possible for me to go for publication with the same result.
Note: From 100 ns MD simulation, 10 snapshots of 1000 frames at 10 ns intervals of whole trajectories were obtained.
There could be several reasons why your MMGBSA result is not as promising as expected. Here are a few possible explanations:
Regarding the possibility of publication, it is important to consider the significance of the findings and the quality of the research rather than just the MMGBSA results. It is possible to publish a paper with negative results or unexpected findings, as long as the research is well-designed and executed, and the results are properly interpreted and discussed. It is important to be transparent about the limitations and potential sources of error in the study.
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