Re: [AMBER] Manually extending the size of the virtual box

From: Jason Swails <>
Date: Mon, 16 Dec 2013 15:12:54 -0500

On Mon, 2013-12-16 at 11:03 -0800, Eugene Yedvabny wrote:
> Hello Dr. Case,
> Unfortunately it looks like igb==6 does not support TIP4P-Ew water model. When I try to run my simulation I get the following error:
> "Cannot use igb>0 with extra-point force fields"
> I was able to run it with TIP3P water model after stripping all the solvent and then solvating a shell of TIP3PBOX in tleap. I would prefer, however, to keep the position of the water molecules as they are in my original pdb, since they are already minimized and equilibrated. If there an easy way to convert one water model to another and still keep the center of the water molecule at the right position?

If you are OK with switching to TIP3P (or any non-EP water molecules), I
wrote a little ParmEd script that I posted on my wiki awhile ago that
will convert TIP4Pew to TIP3P within a topology file.

Here is the relevant link:

I don't recall seeing any code in the GB code path that specifically
handles extra points, so this may be your only option if you wish to
avoid running into the virtual box problem.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Dec 16 2013 - 12:30:02 PST
Custom Search