[gmx-users] No default Bond types error despite entry in ffbonded.itp

[RAHUL SURESH]

On Mon, Apr 8, 2019 at 7:26 PM Irem Altan <irem.altan at duke.edu> wrote:

> Hi,
>
> Thanks for the input. I’m just trying to get it to run at this point —
> I’ll worry about the box later.
>
> Could you please elaborate on “you haven’t mentioned those entries in the
> right way”? The names of the atoms are correct, it’s listed correctly under
> [ bondtypes ], and the parameters are exactly as taken from the .itp file
> shared by the ATB database. What other mistake could I be making?
>
> Hi.

This error normally occurs during inappropriate naming of atoms. Which
means grompp wasn't able to locate the bond parameter of your system from
the ff. Either you must update your ff files or you have to update the
topology of the files with respect to the ff. I suggest you can have a
clean look regarding the atom type nomenclature of your itp and ff.


PS: As the itp is from ATB, there will be warning regarding non-standard
atomtypes which migh help you here. (not sure).

Regards
Rahul

Best,
> Irem
>
> > On Apr 8, 2019, at 12:53 AM, RAHUL SURESH <drrahulsuresh at gmail.com>
> wrote:
> >
> > On Mon, Apr 8, 2019 at 10:09 AM Irem Altan <irem.altan at duke.edu> wrote:
> >
> >> Hi all,
> >>
> >> I’m trying to add the topology for sucrose manually to the force field,
> >> using the .itp file provided here:
> >>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__atb.uq.edu.au_molecule.py-3Fmolid-3D22625-23panel-2Dmd&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=S7EOHss8_RZKlWBIBOMR1Vs4OXaHjqZJpTXfUtbaKUQ&s=CkJYAWZHHTYNI3wnlNXc9RQG_CIrzjdsHPppXHOI2J8&e=
> >>
> >> I created the box with a sucrose molecule and with some waters, and
> tried
> >> to create a .tpr for energy minimization. However, this gives me the
> error
> >> (and similar ones for all bonds, angles, and dihedrals):
> >>
> >> ERROR 1 [file topol.top<
> https://urldefense.proofpoint.com/v2/url?u=http-3A__topol.top&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=S7EOHss8_RZKlWBIBOMR1Vs4OXaHjqZJpTXfUtbaKUQ&s=68yuQVcW74WRMsG1aWudIXVnLZYVSfzkrPYBu79MDeA&e=>,
> line 79]:
> >>  No default Bond types
> >>
> >
> > Which actually means you haven't mentioned those entries in the right
> way.
> >
> >
> >>
> >>
> >> Line 79 refers to the bond between the 1st and the 2nd atom, which are
> >> types HC and C, respectively. So I added this bond to ffbonded.itp,
> using
> >> the info provided in the link to the ATB database above:
> >>
> >>  HC C          2    0.1090    1.2300e+07 ; sucrose HC-C
> >>
> >> However, I still get the same error. What am I missing?
> >>
> >> I can suggest an alternative approach if you are simulating only sucrose
> > molecule in the water box.
> >
> > 1. Construct a PDB with only one water molecule.
> > 2. Use pdb2gmx
> > 3. Then follow the protein-ligand tutorial
> >
> > Hope this work
> >
> > Best,
> >> Irem
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> >
> >
> >
> > Regards
> > Rahul
> >
> >
> > --
> > *Regards,*
> > *Rahul *
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-- 
*Regards,*
*Rahul *