[gmx-users] Restraining water molecule

Justin Lemkul jalemkul at vt.edu
Thu Mar 21 13:12:51 CET 2013



On 3/21/13 8:10 AM, neeru sharma wrote:
>>
>> 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
>>>>
>>>> ========================================
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> --
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>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>>> 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.
>

They're not restraints, they're constraints.  SETTLE fixes the internal geometry 
of the water molecule.  In the .itp file for the special water molecule, you 
need a [constraints] directive.  Consult the manual for content and format.

-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

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



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