Re: [AMBER] parmchk2 multiple parameters

From: Andreas Gavrielides <>
Date: Mon, 19 Dec 2016 17:47:51 +0000

Thank you very much for the very useful insight on the parmck2 output and I would like to have a follow-up question:

If I want to use the frcmod and gaff parameters in general for use in my own codes as well as other molecular dynamics codes how do I use the two prameters properly to derive one parameter for each specified dihedral ?

Thank you again very much for your reply in advance.

Andreas Gavrielides

Doctorant au CIRIMAT-INP Toulouse

SURF Equipe


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From: David Case <>
Sent: Monday, December 19, 2016 6:39 PM
To: AMBER Mailing List
Subject: Re: [AMBER] parmchk2 multiple parameters

On Mon, Dec 19, 2016, Andreas Gavrielides wrote:
> If parmchk2 gives me multiple parameters for a dihedral angle which one
> should I take? Should I select one value or use both values and if both
> values are to be used how do I use them correctly? Thank you very much
> for your help in advance.

parmchk2 is suggesting a torsion parameter with multiple Fourier terms, i.e.
multiple periodicities. You should use the parameters exactly as they are
written (i.e. load the provided frcmod file into tleap.) The presence of
multiple periodicities is signalled by negative values in that column.


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