lec8

Molecular dynamics simulation of proteins with ligand
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Like MDS without ligand, this too is comprised of two main steps: preparation and MDS run. Like before, preparation comprised of several steps:

1) Cleaning the Protein:
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This step is just like the one before. But this time there will be two files. One is the old [protein].pdb file. The other one is the [ligand].pdb. This ligand
file is generated the same way by cleaning the file, but this time, everything except the ligand in question is cleaned.

2) Applying the forcefield:
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Force field have to be applied seperately, to the [protein].pdb file and to [ligand].pdb file. The ligand file have to be modified in certain ways to make it 
adequate for the application of the forcefield. After applying the forcefield, these two files have to be merged.

3) After the applicaiton of the forcefield, the usual steps like defining the box, adding water, nutralization etc comes along.

4) Then comes temperature and pressure equilibration.

5) Then the final MD simulation.