AMBER Archive (2003)

Subject: AMBER: Fluorine in GBSA

From: aini_at_UMDNJ.EDU
Date: Mon Nov 24 2003 - 08:38:38 CST

Dear Ambers,

   I am trying to run a MD simulation on protein-ligand complex using GBSA. One
thing troubled me is that my ligand has F atom and sander doesn't have surface
area parameter for this atom. If I use gbsa = 0, the sander will run. My
question is if this kind of simulation (gbsa = 0) is reasonable using GB. And do
I need to modify some other parameters to accomadate gbsa = 0.
Thank you very much!

aini

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