Analysis of Protein-Ligand Molecular Dynamics (namd/VMD)
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3 months ago

Hello everyone :) I've been trying to learn methods/techniques related to CADD for the past 5-6 months, I'm actually looking for help to understand the molecular dynamics protocol for a protein-ligand complex, I've checked the online tutorials, to some extend they explain how to run such simulations but (unfortunately) not much about making sense of the results, I'm from a life science background so computation is still a bit confusing for me, as a background, here is a layout of my work:

  • I searched for natural compounds that are similar to a drug (Y) that inhibits my enzyme (X)
  • I performed molecular docking and I established that there is a potential affinity between X and Y
  • Now I want to validate my docking results using molecular dynamics so I learned how to use namd/vmd which (OMG) took ages but I have passed all the errors and now I'm able to perform basic/standard md runs, I have the outputs as .dcd .coor .log .xcs ... , the simulation I performed involved 25k minimization (nvt) and 100K md run.

I've checked some tutorials online but (to the best of my knowledge) couldn't find a complete protocol explaining how to check the stability of the protein-ligand compound or finding their free binding energies to compare or any meaningful analysis that could serve as a validation (or disproof) of my docking results. Some suggested to perform a md on the ligand alone and compare the results to the protein-ligand one, it made logical sense but I couldn't figure how to do that, any suggestions both theoretical or (preferably) computational/practical would help me a lot, thanks in advance, stay safe :)

molecular dynamics namd vmd docking • 208 views
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3 months ago
isik ▴ 10

You can use MM-GBSA and free energy perturbation methods to validate your docking results.

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Thank you Mr.Işık, I've checked https://doi.org/10.1021/acs.chemrev.9b00055 and 10.1517/17460441.2015.1032936. MM-GBSA indeed sounds like a promising methodology I could use, however I couldn't find any protocol on how to apply it on vmd/namd outputs, could you suggest any protocol or tutorial I could use or provide some assistance ? thanks again :)

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