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
