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)
<http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/cgenff_charmm2anton.py>
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
#endif
again obtained the same error. Please help me out here.
With Regards
Upendra N
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