[gmx-users] Ligand breaks during energy minimization

Nikhil Maroli scinikhil at gmail.com
Fri Mar 25 06:46:45 CET 2016

Soumya Lipsa Rath <soumyalipsabt at ...> writes:

> 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 
> After solvation and addition of ions, when I am trying to run an energy
> minimization, my ligand breaks into pieces.

There wont be any bond breaking or formation in MD,observe carefully.if 
your saying the ligand going apart from the protein-there are many methods 
to fix it ,
> Could anyone please give insights on what I might be doing wrong?
> Thanks,
> Soumya

More information about the gromacs.org_gmx-users mailing list