Re: [AMBER] Implicit MD run

From: Aditya Padhi <>
Date: Mon, 19 Mar 2012 16:41:35 +0530

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,
AMBER mailing list
Received on Mon Mar 19 2012 - 04:30:02 PDT
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