Re: [AMBER] Implicit MD run

From: Carlos Simmerling <>
Date: Tue, 20 Mar 2012 07:02:13 -0400

look at this nice tutorial from the Rizzo lab

On Tue, Mar 20, 2012 at 1:52 AM, Aditya Padhi <> wrote:

> 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
> simulations.
> Thanks for your valuable suggestions.
> Regards
> Aditya.
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Received on Tue Mar 20 2012 - 04:30:03 PDT
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