[gmx-users] Re: gmx-users Digest, Vol 107, Issue 81

[neeru sharma]

> 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:
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> 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
>
> ========================================
>
>
> ------------------------------
>
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> 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?


--Neeru