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

[Justin A. Lemkul]

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
>>
>>         -- 
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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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