Dear Mark,<br><br>A million thanks. Problem is solved. <br>Finally,<br>Select a continuous group of solvent molecules:<br>...<br>Group 12 ( Water) has 126219 elements<br>Group 13 ( SOL) has 126219 elements<br>
<br>Which one should I choose 12 or 13?<br><br><b>Final topol.top file:<br><br><br></b>; File 'topol.top' was generated<br>; By user: onbekend (0)<br>; On host: onbekend<br>; At date: Tue Jan 25 10:12:14 2011<br>
;<br>; This is a standalone topology file<br>;<br>; It was generated using program:<br>; pdb2gmx - VERSION 4.5.3<br>;<br>; Command line was:<br>; pdb2gmx -f 3MOA.pdb -water spc -ter <br>;<br>; Force field was read from the standard Gromacs share directory.<br>
;<br><br>; Include forcefield parameters<br>#include "gromos43a1.ff/forcefield.itp"<br><br>; Include chain topologies<br>#include "topol_Protein_chain_P.itp"<br>#include "topol_Protein_chain_L.itp"<br>
#include "topol_Protein_chain_H.itp"<br><br>; Include water topology<br>#include "gromos43a1.ff/spc.itp"<br><br>#ifdef POSRES_WATER<br>; Position restraint for each water oxygen<br>[ position_restraints ]<br>
; i funct fcx fcy fcz<br> 1 1 1000 1000 1000<br>#endif<br><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 41771<br>
<b>CL 8<br></b><br><br><br><div class="gmail_quote">25 Ocak 2011 13:13 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></div><div class="im"><blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite">
<div>Dear Mark and Emanuel,<br><br>I am sending the ions.tip and the topol.top files. <span lang="en"><span title="Alternatif çevirileri görmek için tıklayın">Everything</span> <span title="Alternatif çevirileri görmek için tıklayın">seems</span> <span title="Alternatif çevirileri görmek için tıklayın">ok. </span></span><span lang="en"><span title="Alternatif çevirileri görmek için tıklayın">Any problem about</span> <span title="Alternatif çevirileri görmek için tıklayın">these files</span><span title="Alternatif çevirileri görmek için tıklayın">?</span></span></div>
</blockquote><br></div>No. So one of the other #include files is erroneously defining ion molecule types. See <a href="http://www.gromacs.org/Documentation/Include_File_Mechanism" target="_blank">www.gromacs.org/Documentation/Include_File_Mechanism</a>. Go and read them and fix it.<br>
<br>As the link I sent last time hinted, you need to name *molecules* in the [molecules] directive. Look carefully at the *molecule* name of chloride where it is defined.<br><font color="#888888"><br>Mark</font><div><div>
</div><div class="h5"><br><blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div><br>
<br>By the way, I am using the Gromacs 4.5.3.<br>Force Field 43a1<br><br><div class="gmail_quote">25 Ocak 2011 12:03 tarihinde Emanuel Peter <span dir="ltr"><<a href="mailto:Emanuel.Peter@chemie.uni-regensburg.de" target="_blank">Emanuel.Peter@chemie.uni-regensburg.de</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 style="font-family: Tahoma,sans-serif; font-size: 13px;">Hello,<br><br>You have to look into your ions.itp which is included in your top-file by #include ions.itp.<br>
There all the types of ions have to be defined.<br>The atom-types which you can see in the ions.itp, you will<br>find in the ff"your-forcefield".itp where your atomtypes are defined.<br>On top of your .top file the Atomtype-itp-file is included.<br>
All these files are normally placed in /usr/share/gromacs/top/.<br>But you also can place them into your current directory.<br><br>Bests,<br><br>Emanuel<br><br>>>> Mark Abraham 25.01.11 10.48 Uhr >>><div>
<div><br></div><div><br>
<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>Dear Mark,<br><br>I looked at gromacs mail list but <span lang="en"><span title="Alternatif çevirileri görmek için tıklayın">I could not find</span> <span title="Alternatif çevirileri görmek için tıklayın">a proper</span> <span title="Alternatif çevirileri görmek için tıklayın">solution .</span></span><span lang="en"><span title="Alternatif çevirileri görmek için tıklayın">What</span> should <span title="Alternatif çevirileri görmek için tıklayın">I</span> <span title="Alternatif çevirileri görmek için tıklayın">add</span> <span title="Alternatif çevirileri görmek için tıklayın">to the .top file</span><span title="Alternatif çevirileri görmek için tıklayın">?</span></span> Please look at the following reconstructed1 .top and reconstructed1 .top files<br>
<span lang="en"><span title="Alternatif çevirileri görmek için tıklayın"><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></b></div></blockquote><br>I don't have any knowledge of the context, so can't answer. It looks to me like you are mixing copies of ions.itp from multiple sources. Don't. Use the one for the force field you are targetting. pdb2gmx generated the right invocation - all you should have to do is use that by generating correctly-named ions. See<a href="http://www.gromacs.org/Documentation/Gromacs_Utilities/genion" target="_blank"> http://www.gromacs.org/Documentation/Gromacs_Utilities/genion</a><br>
<br>Mark<br><br><blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div><b>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" target="_blank">mark.abraham@anu.edu.au</a>></span> yazdı:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><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><br></div><div><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>
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