<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Carefully check the number of all the molecules listed in your topology file [ molecules ] section and verify if that corresponds exactly to the number of atoms in your coordinate file. You have added some extra atoms/molecules in the topology.<div><br class="webkit-block-placeholder"></div><div>Venky<br><div> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Verdana; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Verdana; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Calisto MT'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: 'Calisto MT'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: 'Calisto MT'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Verdana; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="font-family: Verdana; font-size: 12px; "><font class="Apple-style-span" color="#7F7F7F">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</font></div><div style="font-family: Verdana; font-size: 12px; "><span class="Apple-style-span" style="font-family: Verdana; font-size: 12px; "><span class="Apple-style-span" style="font-family: Verdana; font-size: 12px; "><font class="Apple-style-span" color="#7F7F7F">Venky Krishnamani</font></span></span></div><div style="font-family: Verdana; font-size: 12px; "><span class="Apple-style-span" style="font-family: Verdana; font-size: 12px; "><span class="Apple-style-span" style="font-family: Verdana; font-size: 12px; "><font class="Apple-style-span" color="#7F7F7F">Dr.Janos K. Lanyi Lab,</font></span></span></div><div style="font-family: Verdana; font-size: 12px; "><span class="Apple-style-span" style="font-family: Verdana; font-size: 12px; "><span class="Apple-style-span" style="font-family: Verdana; font-size: 12px; "><font class="Apple-style-span" color="#7F7F7F">D320, Medical Sciences I</font></span></span></div><div style="font-family: Verdana; font-size: 12px; "><span class="Apple-style-span" style="font-family: Verdana; font-size: 12px; "><span class="Apple-style-span" style="font-family: Verdana; font-size: 12px; "><font class="Apple-style-span" color="#7F7F7F">University of California, Irvine</font></span></span></div><font class="Apple-style-span" color="#7F7F7F">Irvine, CA 92697</font></span></span></span><div><font class="Apple-style-span" face="Verdana" size="3"><span class="Apple-style-span" style="font-size: 12px; "><font class="Apple-style-span" color="#7F7F7F">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</font></span></font></div></span></div></span></div></span> </div><br><div><div>On Feb 22, 2008, at 11:14 PM, s lal badshah wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi,<br>I am new to GROMACS.Currently I am working on a protein.For minimization I prepare file and when I gave the command in the shell the following output comes:<br><span style="font-weight: bold;">Fatal error:</span><br style="font-weight: bold;"><span style="font-weight: bold;">number of coordinates in coordinate file (2a5f_b4ion.pdb, 40183)</span><br style="font-weight: bold;"><span style="font-weight: bold;"> does not match topology (2a5f.top, 40612)</span><br style="font-weight: bold;">Please guide me what path I should follow to correct it.<br>Regards,<br>lal badshah<br><p> Send instant messages to your online friends <a href="http://uk.messenger.yahoo.com">http://uk.messenger.yahoo.com</a> _______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. 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