Dear Mark,<br><br>I looked at gromacs mail list but <span id="result_box" class="short_text" lang="en"><span title="Alternatif çevirileri görmek için tıklayın" class="hps">I could not find</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">a proper</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">solution .</span></span><span id="result_box" class="short_text" lang="en"><span title="Alternatif çevirileri görmek için tıklayın" class="hps">What</span> should <span title="Alternatif çevirileri görmek için tıklayın" class="hps">I</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">add</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">to the .top file</span><span class="" title="Alternatif çevirileri görmek için tıklayın">?</span></span> Please look at the following reconstructed1 .top and reconstructed1 .top files<br>
<span id="result_box" class="short_text" lang="en"><span title="Alternatif çevirileri görmek için tıklayın" class="hps"><br></span></span>I have error as the following reconstructed1 .top file:<br>
<b>Fatal error:</b><br>
moleculetype CU1 is redefined<br><br>
I have error as the following reconstructed2 .top file:<br>
<b>Fatal error:</b><br>
No such moleculetype CL-<br><b><br>Original .top file:</b><br>; Include topology for ions<br>#include "gromos43a1.ff/ions.itp"<br><br>[ system ]<br>; Name<br>GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water<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 41779<br>
<br><b>reconstructed1 .top file</b><br>; Include topology for ions<br>#include "gromos43a1.ff/ions.itp"<br><b>#include "ions.itp"</b><br><br>[ system ]<br>; Name<br>GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water<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 4177<b>1</b><br>
CL- <b>8</b><br><b>reconstructed2 .top file</b><br>; Include topology for ions<br>#include "gromos43a1.ff/ions.itp"<br><b></b><br>[ system ]<br>; Name<br>GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water<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 4177<b>1</b><br>
CL- <b>8</b><br><br><br><div class="gmail_quote">25 Ocak 2011 10:49 tarihinde Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span> yazdı:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im"><br><br><span>On 01/25/11, <b>ahmet yıldırım </b> <<a href="mailto:ahmedo047@gmail.com" target="_blank">ahmedo047@gmail.com</a>> wrote:</span><blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite">
<div>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></div>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>
<font color="#888888"><br>Mark</font><div><div></div><div class="h5"><br><br><blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div><br><br><span lang="en"><span title="Alternatif çevirileri görmek için tıklayın">Below is</span> <span title="Alternatif çevirileri görmek için tıklayın">the first</span> <span title="Alternatif çevirileri görmek için tıklayın">and</span> <span title="Alternatif çevirileri görmek için tıklayın">final version</span> <span 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 "ions.itp"</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>
</div></blockquote>
</div></div><br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>