[gmx-users] error in grompp step

[Justin Lemkul]

On 3/19/18 10:05 AM, Upendra N wrote:
> 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.

Don't use old parameters unless you specifically need them. C36m is an 
improvement over C36.

Your problem is probably that the script produced a .prm file with 
additional parameters needed by your ligand. You need to #include this 
in your topology.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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