Re: [AMBER] Implicit MD run

From: Carlos Simmerling <>
Date: Mon, 19 Mar 2012 08:42:34 -0400

are you simulating DNA? that's a DNA tutorial.
I strongly suggest that you don't just follow a tutorial designed to tech
you how to change certain flags (and in the end I believe the tutorial
suggests that this GB model does not work well in the example) but follow
instead the literature. find one or more articles that successfully do what
you are trying to do. read their methods carefully. then, use the tutorials
to help you understand which specific flags will let you use a method such
as that outlines in the article. a good article will tell you all of the
options that they set, including the radii set that was used (look at the
Leap manual for PBradii- they are used for GB as well).

On Mon, Mar 19, 2012 at 7:11 AM, Aditya Padhi <> wrote:

> Dear Dr. Simmerling,
> I have followed the below mentioned tutorial
> to carry out the
> Implicit MD simulation of my protein of interest. I have used igb=5 for the
> same. Before running the above steps mentioned in the tutorial, I have
> prepared the protein with the following set of commands:
> tleap -s -f leaprc.ff99SB
> mol = loadpdb protein.pdb
> addions mol Na+ 0
> saveamberparm mol protein_lig.prmtop protein_lig.inpcrd
> But I am still not getting which radii you are mentioning about. Please
> provide me some additional options so that I can mail you back.
> Thanking you,
> Regards
> Aditya.
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Received on Mon Mar 19 2012 - 06:00:03 PDT
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