Re: [AMBER] problem with extraction of potential energy for the ligand

From: Maryam Hamzehee <>
Date: Wed, 10 Jun 2015 19:03:44 +0000 (UTC)

I do not know why all of the linebreaks are messed up, please see the attached file of output. I will try your suggestion to see what happens.
Many thanksMaryam


     On Wednesday, 10 June 2015, 22:46, Jason Swails <> wrote:

 I don't know how you're formatting your email, but all of the linebreaks
are messed up, so the output looks like a jumbled mess.  It's difficult to
make sense of your output.

On Wed, Jun 10, 2015 at 1:45 PM, Maryam Hamzehee <>

> Dear Bill
> Many thanks for the email. When I produce the lig.traj  (trajectory of the
> ligand) using "no box" option, sander gives error message saying that it
> can't read the box from the mdcrd file. That's why we used the box. How we
> can ignore the box?

​If you want gas phase electrostatics and your system does not have a
periodic box, you should set igb to 6 in your input file and ntb to 0
(which you seem to be doing) -- *especially* when you are using imin=5 to
analyze a trajectory.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Jun 10 2015 - 12:30:03 PDT
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