Hi,
I am working on a protein-ligand complex that requires steering of the
docked ligand into the protein's active site to study the mechanism of
binding. I am following the Non-equilibrium Free Energy (NFE) module to do
the same. I am following the tutorial,
https://ambermd.org/tutorials/advanced/tutorial10/index.php, and want to
apply the LCOD CV for my case.
As mentioned, I must use even numbers of atoms in the cv_i list. Let's say
I have a list of 8 atom indices; how do I place the atom indices in the
cv_i list? Is it like the dissociation list, followed by the formation ones
as shown, or can I put the pair of atoms at random?
*With regards,*
*Satyajit Khatua*
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Received on Sun Oct 08 2023 - 08:30:02 PDT
