Re: [AMBER] Lennard-Jones Parameters for Each Atom

From: Jason Swails <>
Date: Fri, 5 Sep 2014 09:59:08 -0400

On Fri, Sep 5, 2014 at 9:46 AM, Uday Midya <> wrote:

> Hi All
> I require the numerical value of *epsilon* and *sigma *for each atom in my
> system. I find in amber topology file that their product is given in the
> *Aij* and *Bij* form for each pair of atom type. Can any one suggest me how
> to get the *sigma *and* epsilon*?

​ParmEd will print them out for you. Just use the "printDetails :*"
command to print the details on all of the atoms in the system. For
example: -p prmtop << EOF
printDetails :*

It will list (among many other properties), the LJ radius and LJ depth.
 The sigma parameter ​is related to the radius by "radius = 2^(1/6)*sigma"
and the well depth is epsilon.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Sep 05 2014 - 07:00:03 PDT
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