Re: [AMBER] Can I use paramfit for MM scan?

From: David Cerutti <>
Date: Sat, 11 Apr 2020 06:53:15 -0400

The mdgx program will do what you want: see this tutorial on conformational

Pretty much all you'll need is a topology, a starting coordinates file, and
a simple input file where you give it the atom names in ambmasks (i.e. :1.CA,
or :2.OG). It will infer what type of restraint you want based on how many
atoms you tell it are part of the restraint (two for bonds, three for angle
restraints, etc.).

It can provide regular or randomized sampling over a specified interval.
The conformation sampling feeds into force field development protocols:


On Fri, Apr 10, 2020 at 9:31 PM Elif Çiğdem Calvin <>

> Hello,
> in paramfit tutuorial, dihedral angles are changing randomly with an *.sh
> file then single point energy calculation performes via this angles ( Imean
> structures).
> I wonder what if I change dihedral angles regularly (for example 5 degree
> step : 5-10-15-20 ...180 exc..) and then I calculate single point energies
> and I prepare quantum_a.dat file with this data; can I obtain MM scan in
> the fit_output_energy.dat as (AMber +K) value? or is it wrong to use this
> way to calculate MM scan for a dihedral?
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Received on Sat Apr 11 2020 - 04:00:02 PDT
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