[gmx-users] Ligand breaking in to two

Mark Abraham mark.j.abraham at gmail.com
Mon Oct 21 12:47:46 CEST 2013

Sounds like issues with
strategies for coping found there.


On Mon, Oct 21, 2013 at 9:31 AM, MUSYOKA THOMMAS <
mutemibiochemistry at gmail.com> wrote:

> 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
> --
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