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

[ahmet yıldırım]

I tried SOL 44453 but I still the same error

01 Nisan 2011 15:11 tarihinde Mark Abraham <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>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
>>
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>
>
>
> --
> Ahmet YILDIRIM
>
>
>
> --
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-- 
Ahmet YILDIRIM
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