Re: [AMBER] PARMED Charmber User Warning Quesiton

From: Jason Swails <>
Date: Tue, 14 Sep 2021 16:49:39 -0400

On Mon, Sep 13, 2021 at 7:18 AM Matthew Guberman-Pfeffer <> wrote:

> Dear Amber Community,
> I’m trying to generate a prmtop from psf/pdb for a heme containing system,
> and the chamber utility of ParmEd is giving me the below warnings:
> UserWarning: WARNING: Ignoring "DELETE ACCE NE2" because entity type ACCE
> not used.
> UserWarning: WARNING: Ignoring "DELETE ANGLE 1NA 1FE 1NC 1NB 1FE 1ND"
> because entity type ANGLE not used.
> UserWarning: WARNING: Ignoring "DELETE ANGLE 2NA 2FE 2NC 2NB 2FE 2ND"
> because entity type ANGLE not used.

> Is the following interpretation right: The residue definitions says to
> delete these angles, and Chamber is ignoring these statements precisely
> because the angles aren’t used.

> Can these warning safely be ignored?

Yes, these can be safely ignored. The residue definitions are actually
irrelevant to `chamber`, since they're just used by CHARMM when building
the PSF. Since chamber requires the PSF to be generated already, they have
no effect.

Also, what validation step(s) should I take to make sure the generated
> prmtop is good?

You can compare the gas phase single-point energies produced by both Amber
and CHARMM (if those match, the forces will match as well from my
experience). That's really the only way to definitively tell. Just be
careful that the coordinate files you're using in both cases have the same

A method that is almost as reliable is to compute an energy using ParmEd
(via OpenMM) using both the Chamber-generated prmtop and the original PSF
files (use the same coordinate file). If those energies match, then the
conversion is correct.

Hope this helps,

Jason M. Swails
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Received on Tue Sep 14 2021 - 14:00:02 PDT
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