Dear Dr. Simmerling,
I have followed the below mentioned tutorial
http://ambermd.org/tutorials/basic/tutorial1/section4.htm 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 - 04:30:02 PDT
