Is it a problem with an index file? is 'Water' an index group, and if
so, is is contiguous.
Erik
ahmet yıldırım skrev 2011-04-01 14.15:
I tried SOL 44453 but I still the same error
01 Nisan 2011 15:11 tarihinde Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@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.abra...@anu.edu.au <mailto:mark.abra...@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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-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
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