[AMBER] Can we relax protein and ligand separately?

From: <kurisaki.ncube.human.nagoya-u.ac.jp>
Date: Thu, 10 Mar 2011 10:34:38 +0900

Dear Amber users,

Thank you for kind and useful support at all time.

I would like to relax protein and ligand separately,
although both molecules coexist in the same system.

I can perform the above simulations
if non-bonded interactions (Coulomb and vdW interactions)
were able to be turned off by editing TOPOLOGY file.
For vdW interactions, I believed it possible,
because pair wise interaction by LJ was controlled by "LENNARD JONE" section.
But for Coulomb interactions, I am now considering.

I am most grateful to give me advices for resolution of the problem.

Yours sincerely,

                     Ikuo Kurisaki

I assumed the system was solvated with explicit water.

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Received on Wed Mar 09 2011 - 18:00:04 PST
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