Molecular dynamic simulation of protein- ligand complex. How do I set up a molecular dynamic simulation...

Molecular dynamic simulation of protein- ligand complex.
How do I set up a molecular dynamic simulation for a protein- ligand complex with a cobalt in the 2++ state? In other words, are there topology and parameter files that contain parameter for cobalt ion which are compatible with NAMD?

Expert Solution

If you have got the correct pose from docking result and you have a target in your hand; then, you start MD simulation. So for MD is concerned using NAMD, You cant directly run simulation because the parameters and topology of your ligand are unknown to NAMD.

For that you need to first "Parametrize" your ligand molecules. There are two ways for parametrization . You can use QM calculations using programs like SPARTAN, or you can derive parameters as well as topology of your ligand by analogy using online server Paramchem (https://cgenff.paramchem.org/)

Once you derived topology and parameters for your ligand. you can use LIE (Linear Interaction Energy) method for free energy calculation.

Follow the elementary tutorial in this context at url

http://cinjweb.umdnj.edu/~kerrigje/pdf_files/NAMD-LIE-tutorial.pdf

It is also advised to follow "Parametrizing a novel residue" tutorial at http://www.ks.uiuc.edu/Training/Tutorials/index-all.html#namd before you proceed to LIE..

hopefully this serves the purpose...

gladiator answered 1 year ago

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