Dear User, I am trying to find the RMSD of a single water molecule which showed H-bond interaction with a ligand in a protein-ligand system simulation. The study was to explore the role of water in the binding of the ligand at the receptor. The RMSD of the water molecule (using the protein backbone for fitting) huge variation between 2 to 10 angstrom. VMD visualization showed that the water molecule was basically all over the simulation box and not at the vicinity of the ligand. Is it right to say from this observations that: 1. The H-bonds interaction of ligands with water molecule are transient ? 2. Water molecules are indeed all over the simulation box ? 3. gmx hbond analysis, gmx distance analysis led me to believe that there are interaction with water through out the simulation; just not the same water molecule . Would that be right ?
Will appreciate if you can advise. Thank you. Sincerely, Seke -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
