[gmx-users] Ligand breaking in to two

[Mark Abraham]

Sounds like issues with
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions,
strategies for coping found there.

Mark


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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