[gmx-users] Ligand breaks during energy minimization

Soumya Lipsa Rath soumyalipsabt at gmail.com
Fri Mar 25 01:35:26 CET 2016

Dear gromacs users,

I have a protein-ligand system to simulate. I got the parameters from
CHARMM CGENFF and converted it to gromacs compatible parameters using
"cgenff_charmm2gmx.py" script as Justin had suggested previously.
Following the Protein-ligand tutorial of gromacs closely, I included the
lig.itp and lig.prm file in my original only protein topology file,
modified the output gro file making it a protein-ligand complex gro file.
After solvation and addition of ions, when I am trying to run an energy
minimization, my ligand breaks into pieces.

Could anyone please give insights on what I might be doing wrong?


More information about the gromacs.org_gmx-users mailing list