[gmx-users] Ligand breaks during energy minimization

[Nikhil Maroli]

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 
file.
> 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