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

From: Jason Swails <>
Date: Wed, 10 Jun 2015 14:16:33 -0400

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?

‚ÄčIf 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
AMBER mailing list
Received on Wed Jun 10 2015 - 11:30:03 PDT
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