[gmx-users] The solvent group Water is not continuous

[ahmet yıldırım]

Dear users,

I created nonaminoacid TRS.itp and EDO.itp files using ProDrg Beta.

genion -s em.tpr -o solvated.gro -nname Na -nn 15 -g em.log
select group:13
Fatal error:
The solvent group SOL is not continuous: index[984]=5334, index[985]=5355
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors



01 Nisan 2011 15:17 tarihinde Justin A. Lemkul <jalemkul at vt.edu> yazdı:

>
>
> ahmet yıldırım wrote:
>
>> I tried SOL 44453 but I still the same error
>>
>>
> Are you using some index file that is specifying a discontinuous water
> group? Have you properly re-created your genion input .tpr file from this
> new topology?
>
> -Justin
>
>  01 Nisan 2011 15:11 tarihinde Mark Abraham <Mark.Abraham at anu.edu.au<mailto:
>> Mark.Abraham at anu.edu.au>> yazdı:
>>
>>
>>    On 1/04/2011 11:03 PM, ahmet yıldırım wrote:
>>
>>>    Dear Dr. Mark,
>>>
>>>    I did you said but I have the same error. please look at attached file
>>>
>>>    topol.top:
>>>
>>>    [ molecules ]
>>>    ; Compound        #mols
>>>    Protein_chain_A     1
>>>    Protein_chain_B     1
>>>    SOL               185
>>>    SOL               143
>>>    SOL             44125
>>>    TRS                1
>>>    EDO                1
>>>
>>
>>    OK, well maybe it doesn't like different chunks of the same molecule
>>    even when they're adjacent in order. Try "SOL 44453" instead.
>>
>>    Mark
>>
>>
>>     01 Nisan 2011 14:41 tarihinde Mark Abraham
>>>    <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> yazdı:
>>>
>>>
>>>        On 1/04/2011 10:26 PM, ahmet yıldırım wrote:
>>>
>>>            Dear Justin,
>>>
>>>            I have Fatal Errror:The solvent group Water is not
>>>            continuous. I look at gmx-users mailing list search. I
>>>            also have the same problem.
>>>            You
>>>            said:(
>>> http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html)
>>>            It is exactly what I said; you've proven it. You have
>>>            solvent, ligand, then
>>>            solvent. To use genion (as the program prints out at the
>>>            prompt) you must have
>>>            a *continuous* group of solvent in order to embed ions. If
>>>            you re-arrange the
>>>
>>>            coordinate file and [molecules] section of the topology,
>>>            you can achieve this.
>>>
>>>            How can I do the re-arrange you said? Can you explain a
>>>            little bit?
>>>
>>>
>>>        You need a system topology whose molecules are ordered such
>>>        that all the water is contiguous. That means the order of the
>>>        names of molecule types in your [ molecules ] section of your
>>>        .top can have only one mention of water. Since the order of
>>>        molecules in the coordinate file must match this order, you
>>>        will need to physically reorder your [ molecules ] section,
>>>        and the chunks of molecules in your coordinate file.
>>>        Fortunately, you don't have to renumber those atoms in the
>>>        coordinate file.
>>>
>>>        Mark
>>>
>>>        --         gmx-users mailing list    gmx-users at gromacs.org
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>>>
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>>>
>>>
>>>
>>>
>>>    --     Ahmet YILDIRIM
>>>
>>
>>
>>    --
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>>
>>
>>
>> --
>> Ahmet YILDIRIM
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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>



-- 
Ahmet YILDIRIM
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