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

[Erik Marklund]

Is it a problem with an index file? is 'Water' an index group, and if 
so, is is contiguous.

Erik

ahmet yıldırım skrev 2011-04-01 14.15:
> I tried SOL 44453 but I still the same error
>
> 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
>>
>>         -- 
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>>
>>
>>
>>     -- 
>>     Ahmet YILDIRIM
>
>
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>
>
> -- 
> Ahmet YILDIRIM


-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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