Your oxygens are both being marked as being double bonded in your MOL2
file which makes them carbonyl oxygens. Antechamber though thinks that
the molecule should have an overall charge of -1 (when -nc is not
explicitly set on the command line) while in fact it is +1 because of
N3 having a double bond within the ring.
The flexibility is a matter of the dihedral assignment so the ones
assigned from parmchk2 are better?
On Fri, 14 Apr 2017 20:50:05 +0000
Emilia Pecora-de-barros <empecora.ucsd.edu> wrote:
> Our collaborators believes the oxygen is deprotonated and so the
> molecule has a charge of -1, but I'm skeptical of that. I can try
> parameterizing the neutral protonated molecule, but this shouldn't
> change the error due to bond assignment, should it? I'll probably
> need to manually fix the assignment of this problematic double bond,
> I'm guessing.
>
> Best,
> Emilia
> ________________________________________
> De: Hannes Loeffler [Hannes.Loeffler.stfc.ac.uk]
> Enviado: sexta-feira, 14 de abril de 2017 5:23
> Para: amber.ambermd.org
> Assunto: Re: [AMBER] Incorrect ligand parameterization using GAFF
>
> On Thu, 13 Apr 2017 17:16:07 +0000
> Emilia Pecora-de-barros <empecora.ucsd.edu> wrote:
>
> > region of the frcmod file describing the dihedrals of interest:
> > DIHE
> > cc-ce-cd-cd 1 1.000 180.000 2.000 same as
> > X -ce-ce-X nd-cc-ce-cd 1 1.000 180.000 2.000
> > same as X -ce-ce-X nd-cc-ce-ha 1 1.000 180.000
> > 2.000 same as X -ce-ce-X c -cc-ce-cd 1 1.000
> > 180.000 2.000 same as X -ce-ce-X c -cc-ce-ha 1
> > 1.000 180.000 2.000 same as X -ce-ce-X
> > cd-cd-ce-ha 1 1.000 180.000 2.000 same as
> > X -ce-ce-X
>
> This looks like the output from parmchk. Parmchk2 gives you larger
> barrier heights but also a large penalty score.
>
> DIHE
> cd-cd-ce-cc 4 26.600 180.000 2.000 same as X
> -ce-cf-X , penalty score=136.0 nd-cc-ce-cd 4 4.000
> 180.000 2.000 same as X -ce-ce-X , penalty score=136.0
> nd-cc-ce-ha 4 4.000 180.000 2.000 same as X
> -ce-ce-X , penalty score=136.0 c -cc-ce-cd 4 4.000
> 180.000 2.000 same as X -ce-ce-X , penalty score=136.0
> c -cc-ce-ha 4 4.000 180.000 2.000 same as X
> -ce-ce-X , penalty score=136.0 cd-cd-ce-ha 4 16.000
> 180.000 2.000 same as X -cc-cd-X , penalty score=136.0
>
> Also, antechamber reports:
>
> Info: Bond types are assigned for valence state 1 with penalty of 1
> Total number of electrons: 130; net charge: -1
>
> So some problem with assigning bonds and has your molecule really a
> net charge of -1?
>
>
> Cheers,
> Hannes.
>
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Received on Sat Apr 15 2017 - 04:00:02 PDT
