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 < [email protected]> 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 > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
