MD

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NAMD docs

MD Tutorial:

• 1. Raw Input preparation

     • Open maestro preprocess the structure (capping, protonation, tautomers…) and make sure you do not have any mistake on the output structure.

• 2. Processed input preparation

     • Save 1 pdb called complex.pdb with receptor-ligand and structural water molecules

     • Save 1 mol2 called ligand.mol2 with the already protonated ligand

• 3. Ligand Preparation

     • export AMBERHOME=/shared/opt/AmberTools/amber16/

     • $AMBERHOME/bin/antechamber -i input_name.mol2 -fi mol2 -o output_name.prep -fo prepi -nc charge_of_ligand -c charge_model -at atom_types -j processors_to_use

     • i.e $AMBERHOME/bin/antechamber -i ligand.mol2 -fi mol2 -o ligand.prep -fo prepi -nc -1 -c bcc -at gaff -j 4

• 4. Receptor Preparation

     • $AMBERHOME/bin/pdb4amber -i input_name.pdb -o output_name.pdb

     • i.e $AMBERHOME/bin/antechamber -i complex.pdb -o complex_processed.pdb

     • Read the output and make sure there are no errors in your input

• 5. Parametrize ligand

     • $AMBERHOME/bin/parmcheck2 -i ligand.prep -f prepi -o ligand.frcmod

• 6. AmberTools input

     • cp /shared/data/software/MD/leap.in your_directory

     • fill in the fields indicated on the file

• 7. Build Topology & Coordinates file

     • leap -sf leap.in

     • check the warning outputs and remove the hydrogens from the complex_processed.pdb that they contain clash (as they will be automatically added by tleap) fix other errors.

     • lauch tleap again

• 8. Visualize the ouput complex.pdb and make sure everything looks alright

     • protein is inside the box

     • ligand looks normal