Hi,
I think you want this webpage, which details the file formats:
https://ambermd.org/FileFormats.php
Dihedral parameters are 2/3 of the way down.
It's the periodicity of the torsional barrier:
PN The periodicity of the torsional barrier.
NOTE: If PN .lt. 0.0 then the torsional potential
is assumed to have more than one term, and the
values of the rest of the terms are read from the
next cards until a positive PN is encountered. The
negative value of pn is used only for identifying
the existence of the next term and only the
absolute value of PN is kept.
-Christina
On Thu, Jun 12, 2025 at 11:51 AM Kelly, Katie Lynette via AMBER <
amber.ambermd.org> wrote:
> Hi all,
>
> I am currently editing a .frcmod file for a custom molecule. This
> nucleotide has the dihedral c3-n3-p5-o, for which there are two entries in
> gaff2.dat. I thought that the fourth column, that says -2 for the first
> dihedral and 3 for the second, might help in knowing which values to use,
> but I am unable to figure out what these numbers represent. I was wondering
> if anyone knows why there are two entries for this dihedral and which
> should be used when? I've attached a screenshot of the two dihedrals in
> gaff2.dat for reference.
> Thanks,
> Katie
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
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Received on Thu Jun 12 2025 - 09:00:03 PDT
