[gmx-users] The solvent group Water is not continuous
Mark.Abraham at anu.edu.au
Fri Apr 1 14:11:22 CEST 2011
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
> [ 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.
> 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
> 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
> 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.
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> Ahmet YILDIRIM
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