Re: [AMBER] Implicit MD run

From: Aditya Padhi <>
Date: Tue, 20 Mar 2012 11:22:57 +0530

Dear Dr. Simmerling,
             No, I am simulating a protein and I just mentioned the DNA
tutorial to show that those are the steps I am following for the implicit
solvent MD runs. I am using igb=5 for the same. As I am using igb=5, I
think that the PBRadii is mbondi2. But I have not used this in preparing
the prmtop file. In those tutorials also they have not mentioned about its
use. I think this is indeed a critical parameter. So, can you please
mention how to use the radii parameter? If you have any related article or
tutorial, kindly let me know so that I can start with a fresh set of

Thanks for your valuable suggestions.

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Received on Mon Mar 19 2012 - 23:00:03 PDT
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