===
MD
===

.. toctree::
   :maxdepth: 2

.. figure:: md.gif
    :scale: 100%
    :align: center

Full documentation
------------------------

`NAMD docs <http://www.ks.uiuc.edu/Research/namd/>`_

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