Topic
Molecular Modeling
Molecular Modeling AlphaFold pLDDT and PAE Scores: Is Your Model Good Enough? Read pLDDT from the B-factor column and the PAE plot, then apply a clear go/no-go rule for docking or MD. Learn which… Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling Energy-Minimize a Ligand in Avogadro Before Docking Build, protonate and energy-minimize a ligand in Avogadro, then export a clean file for Vina. Follow the steps and avoid the mistakes… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling DCCM Analysis of a GROMACS Trajectory, Step by Step Compute and read a dynamic cross-correlation matrix from a GROMACS run with Bio3D, ProDy or NumPy. Follow the exact commands and fix… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling Per-Residue Energy Decomposition with gmx_MMPBSA Turn one MM-GBSA number into a per-residue breakdown. Set up the decomp namelist, read the output and name your hotspot residues with… Dr. Abdul Rajjak Shaikh 15 min read Molecular Modeling How to Extract a Single Chain from a PDB File Pull one chain out of a multi-chain structure with PyMOL, ChimeraX, Biopython or the command line, then check it survives pdb2gmx. Start… Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling GROMACS and AutoDock Vina on Mac: Apple Silicon Setup Install GROMACS, AutoDock Vina, Open Babel and PyMOL natively on an Apple Silicon Mac. No Rosetta, no MGLTools. Follow the verified setup. Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling SwissDock Tutorial: Dock a Ligand to a Protein Online Dock a ligand to a protein in your browser with SwissDock: pick AC or Vina, set the box, read the scores. Follow… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling Protein-Ligand Interaction Energy in GROMACS (Rerun Guide) Compute Coulomb and LJ protein-ligand interaction energy in GROMACS with energygrps, mdrun -rerun and gmx energy. Follow the exact commands. Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling gmx make_ndx Tutorial: Index Groups for Protein-Ligand MD Build Protein_LIG, ligand heavy-atom and pocket index groups with gmx make_ndx, script them, and fix the grompp group errors. Follow each step. Dr. Abdul Rajjak Shaikh 15 min read Molecular Modeling Set Up WSL2 for GROMACS, Vina and Open Babel Install WSL2 on Windows and get GROMACS, AutoDock Vina and Open Babel running in one Ubuntu shell. Follow every command, path and… Dr. Abdul Rajjak Shaikh 14 min read