[gmx-users] Restraining water molecule

[neeru sharma]

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

--Thanks
Neeru