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

[Mark Abraham]

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
>
>     -- 
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> -- 
> Ahmet YILDIRIM

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110401/065155d1/attachment.html>