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

[RAHUL SURESH]

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:
> http://atb.uq.edu.au/molecule.py?molid=22625#panel-md
>
> 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<http://topol.top>, 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 *