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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Is there something about the water molecule that is different to
any standard H2O? If not, then simply use:<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal>genbox_d -cs -box 4.0 6.0 4.0 -maxsol 3200<span
style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Catch ya,<br>
<br>
Dr. Dallas Warren<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Medicinal Chemistry and Drug Action<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Monash Institute of Pharmaceutical Sciences</span><span
style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>,
Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@monash.edu<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>+61 3 9909 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a
nail.</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On
Behalf Of </b>Eric Shamay<br>
<b>Sent:</b> Tuesday, 21 September 2010 10:17 AM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] creating a solvent box<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>This may very well be a simple problem, but I have found
little in the way of documentation that helped me get it to work:<br>
<br>
I'd like to form a box (4x6x4 nm^3) filled with 3200 water molecules. I'd like
to use the water model specified in sw.itp (polarizable & flexible). In the
working directory I have a pdb file that specifies exactly the final system
that I want to use, but I cannot generate a .gro file from this pdb file in
order to run a simulation. I've tried 2 routes to accomplish this:<br>
<br>
1) pdb2gmx - I've attempted to use this program as follows:<br>
'pdb2gmx_d -f sw_box.pdb -o sw_box.gro -i sw.itp'<br>
<br>
This reports a fatal error: Residue 'SW' not found in residue topology database<br>
<br>
Because the sw.itp file defines SW as the molecule name, and again as the
residue name, I assumed that's what I'd want to appear in my pdb file as well.
I've tried every combination of force fields and water model to see if that
would do anything, but to no avail.<br>
<br>
2) genbox - I tried to generate a solvent box using the pdb file as the solvent
definition:<br>
<br>
'genbox_d -cs sw_box.pdb -box 4.0 6.0 4.0 -maxsol 3200'<br>
<br>
This made it look as though it was running, but after a very long time it did
not return and produce a .gro file I could use. It's as if the program just
hung or got stuck in some overly complicated solvation routine. <br>
<br>
I realize that the SW residue is not defined in the standard force fields, and
so that's why I want to include sw.itp. Is there a way to generate this box? <o:p></o:p></p>
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