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

[Paolo Costa]

Dear Justin,

thanks a lot.

Paolo

Il giorno dom 26 apr 2020 alle ore 22:33 Justin Lemkul <jalemkul at vt.edu> ha
scritto:

>
>
> On 4/26/20 3:53 PM, Paolo Costa wrote:
> > Dear Justin,
> >
> > thanks for your extra description. Very nice!
> > Last doubt, which values of "phase" and "pn" should I use for [
> > dihedraltypes ]?
>
> If the force constant is zero, the remaining parameters are irrelevant.
>
> -Justin
>
> > Thanks again.
> >
> > Paolo
> >
> > Il giorno dom 26 apr 2020 alle ore 20:33 Justin Lemkul <jalemkul at 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 <
> 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
> >>>>
> >>>> --
> >>>> ==================================================
> >>>>
> >>>> 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
> >>>>
> >>>> jalemkul at vt.edu | (540) 231-3129
> >>>> http://www.thelemkullab.com
> >>>>
> >>>> ==================================================
> >>>>
> >>>> --
> >>>> Gromacs Users mailing list
> >>>>
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> >>>> posting!
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> >>>
> >> --
> >> ==================================================
> >>
> >> 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
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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> >> send a mail to gmx-users-request at 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
>
> jalemkul at 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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>
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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)