<br><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Sepideh Soltani</b> <span dir="ltr"><<a href="mailto:sepideh.soltani@gmail.com">sepideh.soltani@gmail.com</a>></span><br>
Date: Wed, Apr 7, 2010 at 11:21 PM<br>Subject: help<br>To: <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br><br><br><span style="font-family:arial, sans-serif;font-size:13px;border-collapse:collapse"><div>
Hi all,</div><div><br></div><div>I am running with gromacs 4.0.5. I am trying to do gromacs tutorial for drug-enzyme complex. I did this tutorial step by step but when I used the grompp step befor the energy minimization </div>
<div class="im">
<div>"grompp -f em.mdp -c trp_b4em.gro -p trp.top -o trp_em.tpr"</div></div><div>I found the following error:</div><div class="im"><div>-------------------------------------------------------</div><div>Program grompp, VERSION 4.0.5</div>
</div><div class="im"><div>Source code file: toppush.c, line: 947</div><div><br></div><div>Fatal error:</div></div><div>Atomtype CB not found</div><div>-------------------------------------------------------</div><div><br>
</div>then I found this your answer in mailing list :<div class="im"><br>
The PRODRG server generates topologies for the gmx force field (ffgmx;<br>deprecated!). You most likely want to have a topology compliant with the<br>Gromos96 force fields (e.g. ffG43a2). For this you need to use the beta<br>
version of the PRODRG server.<br>and</div></span><div><span style="font-family:arial, sans-serif;font-size:13px;border-collapse:collapse"><div class="im">finally I used Beta version of the PRODRG and used DRGAPH.GRO instead<br>
of DRGFIN.GRO becase I had another problem:<br><div>-------------------------------------------------------</div><div>Program grompp, VERSION 4.0.5</div><div>Source code file: grompp.c, line: 362</div><div><br></div><div>
Fatal error:</div><div>number of coordinates in coordinate file (trp_b4ion.gro, 14622)</div><div> does not match topology (trp.top, 14612)</div><div>-------------------------------------------------------</div>
</div>
But now when again I used the grompp step befor the energy minimization ("grompp -f em.mdp -c trp_b4em.gro -p trp.top -o trp_em.tpr" ) I have this problem:</span></div><div class="im"><div>-------------------------------------------------------</div>
<div>Program grompp, VERSION 4.0.5</div><div>Source code file: toppush.c, line: 1006</div><div><br></div><div>Fatal error:</div><div>moleculetype CU1+ is redefined</div><div>-------------------------------------------------------</div>
</div><div><span style="font-family:arial, sans-serif;font-size:13px;border-collapse:collapse"><div class="im">Now I don't know Is this change correct? If yes, How can I solve this new problem.<br></div>If not How can I solve previous problem.<div class="im">
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<br>Thank you for your help,<br><br>Hanna<br></div></span></div>
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