Dear all,
I did AMBER simulations on a protein binding with a small organic molecule. Checking the trajectory, I can see that the small organic compounds had PBC effect that it departured from the protein. However, when I used pbc unwrap in vmd program to unwrap the trajectory, the small compound side chains broke here and there. I am wondering how I can unwrap the amber trajectory correctly.
Another question is, under such kind of condition, when I did mmgbsa binding energy calculation on the protein binding with the small organic molecule, will the result be reliable? what should I do in order to get reliable binding energy result? Thank you very much.
Laura
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Received on Wed Nov 02 2022 - 08:30:02 PDT
