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).
> > > _________________________________________________________________
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> ________________________________________________________________
>
> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 21 2019 - 03:30:02 PST
