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 Fri Apr 14 2017 - 14:00:04 PDT
