[gmx-users] Restraining water molecule

[Justin Lemkul]

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
>>
>> ========================================
>>
>>
>> ------------------------------
>>
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>>
>
> 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

========================================