[gmx-users] Restraining water molecule

[Justin Lemkul]

On Wed, Mar 20, 2013 at 8:57 AM, neeru sharma <neeru.bioinfo at gmail.com>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

-- 

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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

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