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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><a href="http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology">http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology</a><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>
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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>vineetha mandlik<br>
<b>Sent:</b> Tuesday, 24 April 2012 7:56 PM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] Error in using gromacs for MD simulation<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">---------- Forwarded message ----------<br>
From: <b>Rossen Apostolov</b> <<a href="mailto:rossen@kth.se">rossen@kth.se</a>><br>
Date: Mon, Apr 23, 2012 at 11:53 PM<br>
Subject: Re: error in using gromacs for MD simulation<br>
To: vineetha mandlik <<a href="mailto:vinee2here@gmail.com">vinee2here@gmail.com</a>><br>
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<o:p></o:p></p>
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<p class="MsoNormal">Please send your questions to the mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">
gmx-users@gromacs.org</a>. This is the administrative mail.<span style="color:#888888"><br>
<br>
<span class="hoenzb">Rossen</span></span><o:p></o:p></p>
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<br>
On 2012-04-23 17.12, vineetha mandlik wrote: <o:p></o:p></p>
<p class="MsoNormal">Respected Sir, <o:p></o:p></p>
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<p class="MsoNormal"> Thanks for your reply. I had written to you previously regarding the error in the grompp command when running the MD simulation of a protein, structure was obtaining using homology modelling approach.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The error reported was : Number of coordinates in coordinate file (z_b4em.gro) does not match that of topology file (z.top). We are however not able to run the nohup command because of the above mentioned error. I m sending you the pdb,top
and gro files along with a file containing the commands and output obtained.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Your help in resolving this issue would be highly appreciated. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Thanking you.<o:p></o:p></p>
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<p class="MsoNormal">Vineetha.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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