I'm not familiar with "prep-specified impropers", maybe others are... I
speculate that your prep file lists improper torsions but you don't have
parameters for them, maybe that's why it fails? does your prep file list
improper torsions?
On Thu, Nov 21, 2019 at 6:13 AM Stefano Motta <stefano.motta.unimib.it>
wrote:
> Still get error (Parameter file was not saved.) (Note that this time you
> don't have the angle warnings.
>
> Stefano
>
> Il giorno gio 21 nov 2019 alle ore 12:00 Carlos Simmerling <
> carlos.simmerling.gmail.com> ha scritto:
>
> > If you include the angles and only get torsion warnings you should still
> > generate the leap output files and be able to do md.
> >
> > On Thu, Nov 21, 2019, 5:49 AM Stefano Motta <stefano.motta.unimib.it>
> > wrote:
> >
> > > The only "warnings" that I have in the leap.log are a list of:
> > >
> > > Residue 0: DOC, Terminal/last, was not found in name map.
> > >
> > >
> > > which I had also when I used a nonbonded version of the force-field for
> > the
> > > NP that worked. (DOC and DOD are organic molecules bound to the NP).
> > Then a
> > > list of
> > >
> > > Could not find angle parameter: Ot3 - Ti6 - Ot3
> > >
> > >
> > > for the angles, then a list of:
> > >
> > > 1-4: angle 551 586 duplicates bond ('triangular' bond) or angle
> ('square'
> > > > bond)
> > >
> > >
> > > Which should be normal given the structure of the NP, then a list of
> > > different
> > >
> > > ** No torsion terms for Ht1-Ot3-Ti6-Ot3
> > >
> > >
> > > For the dihedral. I can get rid of the angle warnings including them in
> > the
> > > frcmod file, but even if I insert a line for Ht1-Ot3-Ti6-Ot3 torsion in
> > the
> > > frcmod, I still get the last torsion warning by tleap.
> > >
> > > I attach the complete leap.log file.
> > >
> > > Best
> > > Stefano
> > >
> > >
> > > Il giorno gio 21 nov 2019 alle ore 11:14 Carlos Simmerling <
> > > carlos.simmerling.gmail.com> ha scritto:
> > >
> > > > For dihedrals you should not get errors, only warnings. Are you sure
> > they
> > > > are errors thet cause leap to stop?
> > > >
> > > > On Thu, Nov 21, 2019, 5:05 AM Stefano Motta <stefano.motta.unimib.it
> >
> > > > wrote:
> > > >
> > > > > Hello,
> > > > >
> > > > > I'm trying to use a force-field for TiO2, with only electrostatic,
> > VdW,
> > > > and
> > > > > bond terms. I decided to create a mol2 file for the TiO2
> nanoparticle
> > > > (NP)
> > > > > and treat the NP as a whole residue (the charges for the NP atoms
> are
> > > in
> > > > > the mol2 file with the connectivity). Then I created an frcmod that
> > > > > contains the mass, bonded and VdW parameters.
> > > > >
> > > > > Anyway it seems that tleap is also searching for angle and dihedral
> > > term
> > > > > (that I don't want to include) and gives me error. Then I included
> > the
> > > > > ANGLE and DIHE terms (putting them to 0) in the frcmod (all the
> > missing
> > > > > parameters):
> > > > > For example in case of angle, a lot of lines like this:
> > > > > Ti6-Ot3-Ti6 0.0 0.0
> > > > > and in case of dihedral, a lot of lines like this:
> > > > > Ti6-Ot3-Ti6-Ot3 1 0.0 0.0 2.0
> > > > >
> > > > > Covering all the possible combinations of Angle and dihedrals.
> > > > > This resolved the problem for angle (tleap is not complaining about
> > > > missing
> > > > > parameters for angles) but not for dihedrals (I still get errors
> even
> > > for
> > > > > dihedrals terms that I have inserted in the frcmod).
> > > > >
> > > > > How can I solve this issue? Is there a way to disable the search
> for
> > > > angle
> > > > > and dihedral terms for this molecule?
> > > > >
> > > > > Thanks in advance
> > > > > Best,
> > > > > Stefano
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > ________________________________________________________________
> > > > >
> > > > > Stefano Motta PhD
> > > > >
> > > > > Email: stefano.motta.unimib.it <s.motta17.campus.unimib.it>
> > > > > *Field of study:* Molecular Modeling, and Proteins Molecular
> Dynamics
> > > > >
> > > > > Università degli Studi di Milano Bicocca
> > > > > Department of Earth and Environmental Sciences
> > > > >
> > > > > Piazza dell'Ateneo Nuovo, 1 - 20126, Milano (Italy).
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> > > >
> > >
> > >
> > > --
> > > ________________________________________________________________
> > >
> > > Stefano Motta PhD
> > >
> > > Email: stefano.motta.unimib.it <s.motta17.campus.unimib.it>
> > > *Field of study:* Molecular Modeling, and Proteins Molecular Dynamics
> > >
> > > Università degli Studi di Milano Bicocca
> > > Department of Earth and Environmental Sciences
> > >
> > > Piazza dell'Ateneo Nuovo, 1 - 20126, Milano (Italy).
> > > _________________________________________________________________
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>
>
> --
> ________________________________________________________________
>
> Stefano Motta PhD
>
> Email: stefano.motta.unimib.it <s.motta17.campus.unimib.it>
> *Field of study:* Molecular Modeling, and Proteins Molecular Dynamics
>
> Università degli Studi di Milano Bicocca
> Department of Earth and Environmental Sciences
>
> Piazza dell'Ateneo Nuovo, 1 - 20126, Milano (Italy).
> _________________________________________________________________
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Nov 21 2019 - 03:30:03 PST
