On Wed, Mar 20, 2013 at 8:57 AM, neeru sharma <[email protected]>wrote:
> Dear gromacs users, > > I am simulating a system of Protein-ion-GTP with One Water molecule. I want > to restrain this system (along with this water molecule) for minimization > and equilibration. > > Everytime I run this by specifying the .itp files, it gives the error of > misplacement as follows: > > *"This probably means that you have inserted topology section > "position_restraints" > in a part belonging to a different molecule than you intended to. > In that case move the "position_restraints" section to the right molecule." > * > > The sequence I am giving in the topology file is like this: > > > > * > ; Include Position restraint file for Protein-ion-GTP-Water > #ifdef POSRES_LIGAND > #include "posre_comp.itp" > #endif > > ; Include ligand topology > #include "gtp.itp" > > ; Include water topology > #include "gromos43a1.ff/spc.itp" > > > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > #endif > > ; Include topology for ions > #include "gromos43a1.ff/ions.itp"* > * > > [ system ] > ; Name > Protein in water > > [ molecules ] > ; Compound #mols > Protein 1 > GTP 1 > SOL 1 > SOL 12179 > NA 8 > * > > Can anybody help me figuring out the issue,where I am doing wrong? Any > suggestion is welcome > > If you want to restrain a single water molecule, it needs to be defined as its own [moleculetype] or as a part of the protein [moleculetype]. Breaking apart a continuous block of water causes problems with the SETTLE algorithm, so you will need to manually specify three constraints (OW-HW1, OW-HW2, and HW1-HW2) for this water molecule, while the remaining bath of solvent would be handled by SETTLE. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
