<br /><br /><span>On 01/25/11, <b class="name">ahmet yıldırım </b> &lt;ahmedo047@gmail.com&gt; wrote:</span><blockquote cite="mid:AANLkTi=AFxLR=_Z0qW-8WUzXbCT30PR1GZS=CJxRrqV8@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html">Hi,<br /><br />In my simulation, total charge of the system is a noninteger number (System has non-zero total charge: 8.000004e+00). I neutralized it with 8 chlorine atoms. <br />Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr<br />
<br />Fatal error:<br />
moleculetype CU1 is redefined<br />is it some thing wrong?</div></blockquote><br />ions.itp defines molecule types for ions. Molecule types cannot be redefined. When you #included ions.itp GROMACS thought you were doing illegal redefinitions. Look back in the .top to find the original definitions, and then take suitable action.<br /><br />Mark<br /><br /><blockquote cite="mid:AANLkTi=AFxLR=_Z0qW-8WUzXbCT30PR1GZS=CJxRrqV8@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><br /><br /><span class="short_text" id="result_box" lang="en"><span class="hps" title="Alternatif çevirileri görmek için tıklayın">Below is</span> <span class="hps" title="Alternatif çevirileri görmek için tıklayın">the first</span> <span class="hps" title="Alternatif çevirileri görmek için tıklayın">and</span> <span class="hps" title="Alternatif çevirileri görmek için tıklayın">final version</span> <span class="hps" title="Alternatif çevirileri görmek için tıklayın">of the .top file</span></span>:<br />
<br />First topol.top File<br /><b>....</b><br />[ molecules ]<br />; Compound        #mols<br />Protein_chain_P     1<br />Protein_chain_L      1<br />Protein_chain_H     1<br />SOL                     10<br />SOL                    127<br />
SOL                    157<br />SOL                 41779<br /><b></b><br /><br />Final topol.top File<br /><b>#include &quot;ions.itp&quot;</b><br /><br />[ molecules ]<br />; Compound        #mols<br />Protein_chain_P     1<br />Protein_chain_L      1<br />
Protein_chain_H     1<br />SOL                     10<br />SOL                    127<br />SOL                    157<br />SOL                 <b>41771</b><br /><b>CL-                         8</b><br /><br /><br /><br /><br /><br clear="all" />
<br />-- <br />Ahmet YILDIRIM<br />
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