[gmx-users] error in grompp step

Upendra N nupendra90 at gmail.com
Mon Mar 19 15:05:21 CET 2018

Dear gromacs users,

 I am doing protein-Ligand simulation using gromacs-4.6.2 with charmm36
forcefield. I have generated protein topology using pdb2gmx and ligand
topology using the CGenFF-webservice and cgenff_charmm2anton.py  (to
convert *.str to *.itp and cordinates)

then I included ligand.itp to the main topology file and appended the
ligand coordinates to the protein coordinates to make the protein-ligand
structure coordinate file. Further steps  such as editconf and genbox went
smoothly. But In the grompp step, I get an error as follows,

*ERROR 13 [file gd2.itp, line 248]:  No default U-B typesERROR 14 [file
gd2.itp, line 258]:  No default U-B types......................ERROR 23
[file gd2.itp, line 371]:  No default Improper Dih. types*

Kindly help to fix this error.

I also tried to defining with     define          = -DUSE_OLD_C36 and
inculded         #ifdef USE_OLD_C36

#include "old_c36_cmap.itp"                      in *.top


again obtained the same error. Please help me out here.

With Regards
Upendra N

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