[gmx-users] Pro-Lig Error

[Najamuddin Memon]

Remove coordinates of ligand from .pdb file as you call coordinates of
ligands two times first from .pdb file and second by putting drg.itp
calling from .top file


On Sun, Oct 6, 2019, 9:30 PM Iman Katouzian <imaneternity at gmail.com> wrote:

> Hello,
>
> I have simulated a protein-ligand file and produced the ligand file by
> antechamber software using the Amber03 force field. All the stages in
> Gromacs were performed correctly without any error however when I ran this
> code :
>
> gmx grompp -f MDP/ions.mdp -c solv.gro -p topol.top -o ions.tpr
> I encounter this error:
>
> Fatal error:
> number of coordinates in coordinate file (solv.gro, 40906)
>              does not match topology (topol.top, 40950)
>
> I just performed my simulation many times but I could not pass this error.
>
> Thanks
>
>
>
> --
>
> *Iman Katouzian*
>
> *Ph.D.** candidate of Food Process Engineering*
>
> *Faculty of Food Science and Technology*
>
> *University of Agricultural Sciences and Natural Resources, Gorgan, Iran*
> --
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