[gmx-users] Ligand breaking in to two

[MUSYOKA THOMMAS]

Dear Users,
I am doing protein-ligand MD simulations. I first prepare the ligand by
adding Hydrogen atoms and setting the charges using UCSF chimera. I
thereafter use acpype to get the ligand's gro,itp and top files. Finally, i
process the protein.PDB file and perform MD simulations. However, when I
combine the ligand and protein gro files and convert the resulting complex
to a PDB file so as to visualise with VMD, the ligand always appears to be
broken in two parts.

Any advice on how to overcome this?

Thanks