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

From: amin sagar <aamin.sagar.gmail.com>
Date: Sat, 3 Jul 2021 20:43:25 +0530

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 topol.top conf1-ions.gro topdir amber99sbws-stq.ff radii mbondi2
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.

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Received on Sat Jul 03 2021 - 08:30:03 PDT
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