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

[Irem Altan]

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?

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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