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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