Dear Justin,

thanks for your extra description. Very nice!
Last doubt, which values of "phase" and "pn" should I use for [
dihedraltypes ]?

Thanks again.

Paolo

Il giorno dom 26 apr 2020 alle ore 20:33 Justin Lemkul <jalem...@vt.edu> ha
scritto:

>
>
> On 4/26/20 2:08 PM, Paolo Costa wrote:
> > 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.
>
> Metals are usually the bridge point between multiple groups and as such
> their dihedrals are all coupled and not generally considered "soft"
> (rotatable). So the conformational energetics of these molecules usually
> involves only bonds and angles in terms of internal parameters.
>
> -Justin
>
> > Thanks again.
> >
> > Paolo
> >
> > Il giorno dom 26 apr 2020 alle ore 20:03 Justin Lemkul <jalem...@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
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalem...@vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
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> >> posting!
> >>
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> >> send a mail to gmx-users-requ...@gromacs.org.
> >
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
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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)
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