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

ahmet yıldırım ahmedo047 at gmail.com
Fri Apr 1 14:03:17 CEST 2011

Dear Dr. Mark,

I did you said but I have the same error. please look at attached file


[ molecules ]
; Compound        #mols
Protein_chain_A     1
Protein_chain_B     1
SOL               185
SOL               143
SOL             44125
TRS                1
EDO                1

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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