[gmx-users] Cyclic peptide - topology reconstruction

[Sarath Chandra]

These errors are telling you that for some of the atoms, the listed
parameter types (error warnings by grompp) are not defined in forcefield
files (eg: ffbonded.itp), Check the atoms and check your corresponding
forcefield files along with the procedure of system set up.

regards,

sarath

-- 
Sarath Chandra Dantu, PhD, ELS
Room No. 606, New BSBE Building
Department of Biosciences and Bioengineering
Indian Institute of Technology Bombay
Powai Mumbai, 400-076, India


On 29 April 2016 at 16:50, Ferdous, Saba <saba.ferdous.13 at ucl.ac.uk> wrote:

> Dear Gromacs Support,
>
> I am writing regarding cyclic peptides simulation. I have gone through
> several discussion on mailing list.
>
>
> https://www.researchgate.net/post/How_to_define_energy_minimization_parameters_for_a_cyclic_peptide_GROMACS
>
> http://permalink.gmane.org/gmane.science.biology.gromacs.user/69673
>
> I have used specbond.dat way to workaround. I have successfully built the
> toplogy but as suggested in one of the above discussion that Its required
> to correct the toplogy to add bonds, angle and dihedrals to define the
> linked connectivity. I am bit unclear that how this should be done. Can I
> get some explanation for that?
>
> I have got following errors at ionization step which suggest that
> certainly above connections are not built properly.
>
> ERROR 1 [file topology.top, line 318]:
>   No default Bond types
>
>
> ERROR 2 [file topology.top, line 1297]:
>   No default Angle types
>
>
> ERROR 3 [file topology.top, line 1300]:
>   No default Angle types
>
>
> ERROR 4 [file topology.top, line 1302]:
>   No default Angle types
>
>
> ERROR 5 [file topology.top, line 1303]:
>   No default Angle types
>
>
> ERROR 6 [file topology.top, line 1779]:
>   No default Angle types
>
>
> ERROR 7 [file topology.top, line 1780]:
>   No default Angle types
>
>
> ERROR 8 [file topology.top, line 1781]:
>   No default Angle types
>
>
> ERROR 9 [file topology.top, line 1800]:
>   No default Proper Dih. types
>
>
> ERROR 10 [file topology.top, line 1801]:
>   No default Proper Dih. types
>
>
> ERROR 11 [file topology.top, line 1802]:
>   No default Proper Dih. types
>
>
> ERROR 12 [file topology.top, line 1803]:
>   No default Proper Dih. types
>
>
> ERROR 13 [file topology.top, line 1804]:
>   No default Proper Dih. types
>
>
> ERROR 14 [file topology.top, line 1805]:
>   No default Proper Dih. types
>
>
> ERROR 15 [file topology.top, line 1806]:
>   No default Proper Dih. types
>
>
> ERROR 16 [file topology.top, line 1807]:
>   No default Proper Dih. types
>
>
> ERROR 17 [file topology.top, line 1808]:
>   No default Proper Dih. types
>
>
> ERROR 18 [file topology.top, line 1809]:
>   No default Proper Dih. types
>
>
> ERROR 19 [file topology.top, line 1810]:
>   No default Proper Dih. types
>
>
> ERROR 20 [file topology.top, line 1811]:
>   No default Proper Dih. types
>
> Many thanks,
> Best regards,
> Saba
>
>
> --
> Saba Ferdous
> PhD Student
> Structural and Molecular Biology
> UCL, UK
> Tel: +44 (0) 20 7679 2303
> http://www.bioinf.org.uk/
> --
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