[gmx-users] Error No default Proper Dih. types

[Paolo Costa]

Dear Justin,

thanks a  lot for your quick reply and useful information.
Thus, I will go through to all the dihedral terms and define zero the
corresponding force constant as you suggested. In any case, I guess it will
be too much work to calculate also the force constant for the torsion angle
rotation.

Thanks again.

Paolo

Il giorno dom 26 apr 2020 alle ore 20:03 Justin Lemkul <jalemkul at vt.edu> ha
scritto:

>
>
> On 4/26/20 1:57 PM, Paolo Costa wrote:
> > Dear Gromacs users,
> >
> > within Amber99 force field I created a new molecule, polyoxometallate, by
> > creating a new .rtp file and modifying the atomtypes.atp, ffnonbonded.itp
> > and the ffbondend.itp. For the ffnonbonded.itp I took the LJ parameters
> > from known works, while the parameters for the bonding interactions I
> > determined by Gaussian together with VFFDT software.
> > I did not insert any parameters for the dihedral angles since the VFFTDT
> > software does not calculated them. However as written in the related
> paper
> > (J. Chem. Inf. Model. 2016, 56, 811−818), *"Torsion angle rotation
> related
> > to metals can often be ignored".*
> > Does somebody knows how to overcome such error in Gromacs?
>
> pdb2gmx generates all possible angles and dihedrals, as determined by
> the bonds that are defined in the .rtp entry. Thus, you likely have
> dihedrals in the topology in which one of the participating atoms is the
> metal. You have to have parameters for all defined interactions, but it
> is true that dihedral terms are not typically used in this case. The
> simplest solution is to define dihedrals with zero force constants so
> they do not contribute to the forces in the system.
>
> -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
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>
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-- 
Paolo Costa, Ph.D.
Postdoctoral Researcher
Department of Chemistry and Biomolecular Sciences
University of Ottawa
10 Marie Curie, Ottawa, ON K1N 6N5, Canada
Room number: DRO 326 (D'Iorio Hall)