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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> >
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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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http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 21 2019 - 03:00:02 PST
