[gmx-users] Issue with protein-ligand simulation

[GAYATHRI S]

Dear all,

I am trying to run a protein-ligand simulation as described in the
tutorial by Justin Lemkul

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/01_pdb2gmx.html

However, while creating a unit cell using editconf command, I encounter a
problem. The output file (box.gro) doesn't contain the ligand coordinates.

The command doesn't give any error and runs smoothly.

But, when I reach the energy minimization step, grompp command gives the
"Number of coordinates in coordinate file does not match topology" error.

Kindly suggest how to fix this issue.

Thank you.

Regards,
Gayathri S.