Re: [AMBER] PARMED Charmber User Warning Quesiton

From: Matthew Guberman-Pfeffer <>
Date: Tue, 14 Sep 2021 19:31:10 -0400

Hi Jason,

Thanks so much for your reply. I have one follow-up question: Are there specific settings I should add to the sander/pmemd input, for example, to modify how 1-4 interactions are treated? I know that if I were to use Amber in NAMD, I’d need to do something like this to get comparable energies.


> On Sep 14, 2021, at 4:49 PM, Jason Swails <> wrote:
> *Message sent from a system outside of UConn.*
> 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
> precision.
> 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
> --
> Jason M. Swails
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Received on Tue Sep 14 2021 - 17:00:02 PDT
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