Dear scholars,
I am currently working on a project involving in silico analysis of some active constituents identified by HPLC. So far,
I have done molecular docking using the extra precision (XP) scoring function of Glide. I further employed MM-GBSA method to calculate the binding free energy of the static complexes. Since I used rigid docking method to explain the binding mode, I performed MD simulation over the course of 100 ns to establish the dynamic behavior/stability of the ligands in the active sites of the receptors using Desmond and communicated the results to a journal.
As a part of the reviewers' comment,
I was asked to perform MM-GBSA calculation of the snapshots or the MD trajectories.
Using maestro interface, I have tried using the output of Desmond but to no avail.
Can anyone assist or suggest any possible assistance?
If any assistance, step by step assistance would be appreciated.
Thank you in advance.
From Desmond trajectory, you can extract your desired binding poses and run it in Prime by selecting receptor and ligand separately in options.
Also, you can run thermal_mmgbsa.py script in terminal or command line which will calculate binding energy for all the frames in trajectory. It takes time.
Thanks
Best
Thank you Prateek. I did this exactly. I ran it on my localhost after extracting the receptor and the ligand. it took me several hours to complete and the output was with a CSV file. Attached here is the screenshot of the output. Please assist
$SCHRODINGER/run thermal_mmgbsa.py xx-out.cms -j energy-calc -start_frame 4000 -end_frame 8000 -step_size 50 -HOST localhost:8 -NJOBS 8 > output
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