Molecular Modeling

Run gmx dssp on your GROMACS trajectory, read the .dat and .xvg outputs, and fix the “do_dssp not found” error that breaks every old tutorial.

Stop running Vina once per compound. Learn the –batch flag, the Open Babel prep loop, and how to pull 40 output files into one ranked table.

Predict how a point mutation changes protein stability with DynaMut2, mCSM and DDMut, and learn to read the ddG sign correctly before you report it.

Dock two proteins in a browser with ClusPro, HDOCK or HADDOCK. Prepare your files, run the job, and learn which model to keep and why.

Mutate a residue in PyMOL, save the mutant correctly, then run a fair wild-type vs mutant MD comparison in GROMACS without overclaiming the result.

Build a protein-in-bilayer system with CHARMM-GUI Membrane Builder, then run the six-step equilibration ladder in GROMACS without rebuilding anything.

Set your GROMACS simulation box with gmx editconf. Choose cubic or dodecahedron, pick the right -d distance, and cut roughly 29 percent of your run time.

Predict a protein’s binding pocket with PrankWeb, fpocket or CASTp, then convert it into the grid box coordinates AutoDock Vina needs.

Learn to run gmx cluster with the gromos method and pull one defensible representative structure from your GROMACS trajectory.

Learn the exact gmx trjconv commands to remove PBC artifacts, center your protein, strip water, and extract single frames before you run any analysis.