Hello everyone. I am new to Molecular dynamics simulations. Presently i am using Desmond for my work. Just out of curiosity i want to ask a question. Is it possible at all to carry out MD simulations of only the ligand binding site, instead of the whole protein, in order to save computational time ?
thank you
No sir we solvate the entire system. As MD mimics the natural environment and while doing so the we might obtain misleading data.
Try reading this:
Article Best Practices for Foundations in Molecular Simulations [Article v1.0]
No sir we solvate the entire system. As MD mimics the natural environment and while doing so the we might obtain misleading data.
Try reading this:
Article Best Practices for Foundations in Molecular Simulations [Article v1.0]
Uddipan Das
theoretically yes, but the rest of the protein definitely will affect on the active site.
I mean if you just keep the active site yes you can do it but maybe if you keep all of the protein it will not work correctly.
you can put restrain for some loops of the protein but not delete them.
Dear Uddipan,
One of the most important things that we have to consider during MD simulations is RMSD value, which usually obtained by calculating the positional change of the C alpha atom of the protein backbone during the simulation. Thus, It won't be possible for us to do MD simulation only at the protein active site since the obtained data would be inaccurate and did not resemble the real protein-ligand complex under the real environment.
I hope this paper will help you. Good luck!
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