Tags » VMD

Protein-Ligand System Preparation for NAMD simulations with VMD/LigParGen

      1.  Add the missing side chains using Modeller and can be done in Chimera, but you need to obtain key to access Modeller service online
      2. Clean the protein i.e, delete solvent and add missing side chains etc using Dock Prep in Chimera by running the following script.
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Computational Chemistry