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

From: Eugene Yedvabny <>
Date: Mon, 16 Dec 2013 17:58:33 -0800

Thank you for the suggestions. I've converted my solvent to TIP3P and igb=6
works now to get rid of the virtual box constraints. Unfortunately my next
step is to run these simulations with Amoeba forcefield, which I imagine
would violate igb=6 requirements. On top of that, I still would like to get
long trajectories with TIP4P-Ew rather than TIP3P.

I am not averse to modifying Amber source to remove error conditions or
even the virtual box. I figure modifying the box dimensions would be the
easier approach than going through igb routines. Could you possibly point
me to where in sander source I would find the virtual box routines and how
to best enlarge the box / ignore escaping molecules?

Lastly, for Amoeba simulations, should I even bother trying to run them in
Amber? I've already reported one issue with the way Tinker writes out
disulfide bridge multipoles, which end up breaking tinker_to_amber. If
sander does not support gas-phase NVE with Amoeba then I'll cut my losses
and try running the simulations in Tinker.

Thank you all for the help you've provided!

Thank you,
Eugene Yedvabny

On Mon, Dec 16, 2013 at 12:12 PM, Jason Swails <>wrote:

> 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.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon Dec 16 2013 - 18:00:03 PST
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