Re: [AMBER] Using ParmEd to convert gromacs truncated octahedron box to amber

From: Jason Swails <>
Date: Sun, 18 Jul 2021 10:42:52 -0400

If the simulation runs with sensible energies and dynamics by changing
IFBOX to 3, then use that. If the density is sensible and the
energies/forces don't have the hallmark signs of particle clashes (very
high energies and forces), then the way that the MD engine is handling the
unit cells is correct. GROMACS stores the unit cell vectors themselves,
not the angles, so ParmEd has to convert to the form Amber uses.


On Sat, Jul 3, 2021 at 11:13 AM amin sagar <> wrote:

> Dear Amber Users/Developers,
> I am using ParmEd to convert a gromacs topology to Amber. The box is a
> truncated octahedron.
> My input is as follows.
> gromber conf1-ions.gro topdir amber99sbws-stq.ff radii mbondi2
> hmassrepartition
> outparm conf1-ions-hmr.parm7 conf1-ions-hmr.rst7
> The rst file generated by ParmEd has the following last line
> 114.2371000 114.2371165 114.2370945 70.5287548 109.4712039 70.5288000
> and the values of IFBOX in parm7 file is 2. I think the values for
> truncated octahedron should all be 109.47.
> If I try to use these files, I get the following error.
> Error: ifbox=2 in prmtop but angles are not correct
> If I change the value of ifbox to 3, I can run the simulation. Is this way
> correct? or should I change the angles?
> I would really appreciate any suggestions.
> Best,
> Amin.
> _______________________________________________
> AMBER mailing list

Jason M. Swails
AMBER mailing list
Received on Sun Jul 18 2021 - 08:00:02 PDT
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