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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I have posted this to the gromacs users emailing list.<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:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">No files came through, generally they are stripped off the emails before being posted to the emailing list. Should never send attachments to an emailing list,
post them to the internet and put the URLs in the email for people to look at if they want to. People can’t comment on what isn’t available for them to see.<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:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Can’t suggest anything more about the error. You simply have to find out why there is a difference between the number of atoms in the .gro file and the number
defined by the .top file. If you have checked your .gro and .top files, what did you find? The fact that you still get a warning stating the numbers are different indicates you have still missed something. And if you are following a tutorial, then you have
done something different to what the tutorial has told you to do. Incorrectly edited a file, used the wrong, old file in a new step etc. Many ways you may have gone wrong.<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:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Is it “1 SOL atom” or 1 SOL molecule? Be very careful with your terminology with things like that, can seem the same to someone starting out, but they are
very different.<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 9903 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""> vineetha mandlik [mailto:vinee2here@gmail.com]
<br>
<b>Sent:</b> Saturday, 28 April 2012 5:30 AM<br>
<b>To:</b> Dallas Warren<br>
<b>Subject:</b> Regarding your reply in gromacs users forum<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
Respected Sir,<br>
<br>
I got your reference from the reply that you have given to the question I put up in Gromacs users forum. First of all I would like to thank you for your reply becos nobody seems to answer the question :) even though I had attached our output files too ...
Sir there is problem running with our gromacs program. We carry out MD simulation of proteins using gromacs version 4.
<br>
<br>
And in that case the error obtained is number of coordinates in topology and coordinate file is not the same. As mentioned in gromacs tutorial we have edited even the SOL atoms in topology file, added required number of ions too...yet the same error repeats.
We have cross checked both our top and gro files also.<br>
<br>
<br>
Somehow we get a difference of 1 SOL atoms extra between the topology and coordinate file and we do not know how to proceed. I would like to ask you if you have any suggestions sir, any commands to vary...<br>
<br>
Commands followed are from the following tutorial:<br>
<br>
<a href="http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf">http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf</a>.
<br>
<br>
<br>
<br>
Thanking you.<br>
Vineetha<br>
Junior research fellow, India<o:p></o:p></p>
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