[gmx-users] Cyclic peptide - topology reconstruction

[Ferdous, Saba]

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/