[gmx-users] Restraining water molecule
neeru sharma
neeru.bioinfo at gmail.com
Thu Mar 21 13:10:25 CET 2013
>
> Message: 1
> Date: Thu, 21 Mar 2013 07:05:44 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Restraining water molecule
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <514AE988.4050902 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 3/21/13 4:29 AM, neeru sharma wrote:
> >> Message: 6
> >> Date: Wed, 20 Mar 2013 09:04:05 -0400
> >> From: Justin Lemkul <jalemkul at vt.edu>
> >> Subject: Re: [gmx-users] Restraining water molecule
> >> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >> Message-ID:
> >> <
> >> CADUqwc5+FotCHpMi0PQEExCNPkBTqa-yb0pX1P889Gy3jzAPuA at mail.gmail.com>
> >> Content-Type: text/plain; charset=ISO-8859-1
> >>
> >> 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
> >>
> >> --
> >>
> >> ========================================
> >>
> >> 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
> >> gmx-users at gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >>
> >> End of gmx-users Digest, Vol 107, Issue 81
> >> ******************************************
> >>
> >
> > I tried restraining the single water molecule by specifying the
> > Protein-Ion-GTP-Water as one index group. The itp file, I used for this
> > water molecule was as follows:
> >
> >
> > *[ moleculetype ]
> > ; molname nrexcl
> > WAT 2
> >
> > [ atoms ]
> > ; nr type resnr residue atom cgnr charge mass
> > #ifndef HEAVY_H
> > 1 O 1 WAT O 1 -0.82 15.99940
> > 2 H 1 WAT H1 1 0.41 1.00800
> > 3 H 1 WAT H2 1 0.41 1.00800
> > #else
> > 1 O 1 WAT O 1 -0.82 9.95140
> > 2 H 1 WAT H1 1 0.41 4.03200
> > 3 H 1 WAT H2 1 0.41 4.03200
> > #endif
> >
> > #ifndef FLEXIBLE
> > [ settles ]
> > ; O funct doh dhh
> > 1 1 0.1 0.16330
> >
> > [ exclusions ]
> > 1 2 3
> > 2 1 3
> > 3 1 2
> > #else
> > [ bonds ]
> > ; i j funct length force.c.
> > 1 2 1 0.1 345000 0.1 345000
> > 1 3 1 0.1 345000 0.1 345000
> >
> > [ angles ]
> > ; i j k funct angle force.c.
> > 2 1 3 1 109.47 383 109.47 383
> > #endif*
> >
> >
> >
> > But, ended with the fatal error:
> >
> >
> > *Fatal error:
> > The [molecules] section of your topology specifies more than one block of
> > a [moleculetype] with a [settles] block. Only one such is allowed. If you
> > are trying to partition your solvent into different *groups* (e.g. for
> > freezing, T-coupling, etc.) then you are using the wrong approach. Index
> > files specify groups. Otherwise, you may wish to change the least-used
> > block of molecules with SETTLE constraints into 3 normal constraints.*
> >
> >
> >
> > Then, I tried removed the settles block:
> >
> > *[ settles ]
> > ; O funct doh dhh
> > 1 1 0.1 0.16330
> >
> > *from the itp file. It then, ran the minimization steps which continued
> for
> > 40 steps. But when I visualized the gro file generated, the conformation
> > and orientation of this particular water molecule was not proper. I
> feel, I
> > the settle section of itp file was not treated properly.
> >
> > Any suggestion how to treat this water molecule?
> >
>
> Yes, read my post again. I already said this would happen and described
> exactly
> what you have to do.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
Dear Justin,
I understood the fact that settle can not be applied more than once. I
removed the settle section from the itp file file, but I am still unable to
get how to apply restraint to OW-HW1,OW-HW2 and HW1-HW2 and where to
include these restraints, either in the protein's itp file or a separate
.itp file for this water molecule.
--Neeru
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