<p class="MsoNormal" style="line-height: normal;"><span style="font-size: 12pt; font-family: "Times New Roman","serif";"><br></span></p><p class="MsoNormal" style="line-height: normal;"><span style="font-size: 12pt; font-family: "Times New Roman","serif";">Hi Justin,</span></p>
<p class="MsoNormal" style="line-height: normal;"><span style="font-size: 12pt; font-family: "Times New Roman","serif";"><br></span></p><p class="MsoNormal" style="line-height: normal;"><span style="font-size: 12pt; font-family: "Times New Roman","serif";">Thank you for your reply.</span></p>
<p class="MsoNormal" style="line-height: normal;"><span style="font-size: 12pt; font-family: "Times New Roman","serif";"><br></span></p>
<p class="MsoNormal" style="line-height: normal;"><span style="font-size: 12pt; font-family: "Times New Roman","serif";">Before I contacted you and do what you
suggested ,<span style=""> </span>I
did the following way:</span></p>
<h1 style="margin-left: 36pt; text-indent: -18pt;"><span style="font-size: 12pt; font-weight: normal;"><span style="">1)<span style="font: 7pt "Times New Roman";">
</span></span></span><span style="font-size: 12pt; font-weight: normal;">Firstly, I created the lipopetide (12 Carbon atoms
(tail) + Val-Val-Ala-Gly-Glu-Arg-Gly-Asp) using ChemDraw and saved as a PDB. </span></h1>
<h1 style="margin-left: 36pt; text-indent: -18pt;"><span style="font-size: 12pt; font-weight: normal;"><span style="">2)<span style="font: 7pt "Times New Roman";">
</span></span></span><span style="font-size: 12pt; font-weight: normal;">Then, I pasted my pdb file to the The Dundee PRODRG2.5
Server (beta) and I got conf.gro and topol.top files. </span></h1>
<h1 style="margin-left: 36pt; text-indent: -18pt;"><span style="font-size: 12pt; font-weight: normal;"><span style="">3)<span style="font: 7pt "Times New Roman";">
</span></span></span><span style="font-size: 12pt; font-weight: normal;">After completing some of the missing information by
hand at the topology file (e.g <span style=""> </span>#include
"gromos53a6.ff/forcefield.itp"..), started the simulation for 10 ns. </span></h1>
<h1><span style="font-size: 12pt; font-weight: normal;">Simulation
went through without an apparent error. But I saw that when I watch the trajectory
at Visual Molecular Dynamics (VMD), some bonds seem much longer than they should
be. </span></h1>
<h1><span style="font-size: 12pt; font-weight: normal;">What
could be the reason for this? I wonder<span style="">
</span>if something ‘s wrong in the above process.</span></h1>
<pre><span style="font-size: 12pt; font-family: "Times New Roman","serif";" lang="X-NONE">Thank you in advance,</span></pre><pre><span style="font-size: 12pt; font-family: "Times New Roman","serif";" lang="X-NONE"> </span></pre>
<pre><span style="font-size: 12pt; font-family: "Times New Roman","serif";" lang="X-NONE">Deniz</span></pre><br><br><div class="gmail_quote">On Wed, Feb 23, 2011 at 3:57 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><br>
<br>
Emine Deniz Tekin wrote:<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>
Hi gromacs users,<br>
<br>
<br>
I am using the gromacs 4.5.3 version. I created a lipopetide which consist of 12 Carbon atoms (tail) connected to Val-Val-Ala-Gly-Glu-Arg-Gly-Asp (residues) using ARGUSLAB and I saved it as a pdb file.<br>
<br>
Then, when I used the following command in gromacs:<br>
<br>
pdb2gmx –f lipopepArgus.pdb (GROMOS96 45a3 force field&spc type water model)<br>
<br>
I got the following error message:<br>
<br>
Fatal error:<br>
<br>
Residue 'DEF' not found in residue topology database<br>
<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
<br>
<br>
As far as I could understand, there is no problem with the residues but there is a problem with the atoms in the tail (12 Carbon atoms, 23 Hydrogen atoms and an Oxygen atom, actually it is called a lauroic acid). These atoms are defined as DEF. I thought I should rename the pdb to the expected name given in the .rtp file of the 45a3 force field for my lipopeptide. But I could not find a parameterization for the lauroic acid. In this case, what shoul I do?<br>
<br>
<br>
At the <a href="http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks" target="_blank">http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks</a> page, I found;<br>
<br>
<br>
*Abbrev.*<br>
<br>
<br>
<br>
*Source*<br>
<br>
<br>
<br>
*2*<br>
<br>
<br>
<br>
*Full Name*<br>
<br>
<br>
<br>
*Formula*<br>
<br>
<br>
<br>
*Specifics*<br>
<br>
LAU<br>
<br>
<br>
<br>
fa.itp<br>
<br>
<br>
<br>
O<br>
<br>
<br>
<br>
lauroic acid<br>
<br>
<br>
<br></div>
C_11 H_23 COOH<div class="im"><br>
<br>
<br>
<br>
-<br>
<br>
<br>
Does using fa.itp file solve my problem? If yes, where can I get this file?<br>
<br>
<br>
</div></blockquote>
<br>
This topology is from the deprecated Gromos87 (hacked) force field called ffgmx. Don't use it. The reasons are described in the manual. What's more, you can't use a standalone topology if your molecule is covalently linked to a peptide. You can't have bonds between different [moleculetypes] (i.e. between topologies) in Gromacs.<br>
<br>
The proper procedure is to parameterize the lauroic acid:<br>
<br>
<a href="http://www.gromacs.org/Documentation/How-tos/Parameterization" target="_blank">http://www.gromacs.org/Documentation/How-tos/Parameterization</a><br>
<br>
or obtain compatible parameters from elsewhere and implement them in your chosen force field:<br>
<br>
<a href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field" target="_blank">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a><br>
<br>
You could use Berger lipid parameters for the lauroic acid moiety, you'll just have to add this residue to the force field. The membrane protein tutorial I wrote will walk you through how to modify the force field properly.<br>
<br>
<a href="http://www.gromacs.org/Documentation/Tutorials#Membrane_Simulations" target="_blank">http://www.gromacs.org/Documentation/Tutorials#Membrane_Simulations</a><br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
I would be so glad if you can help me solve this problem.<br>
Thank you in advance,<br>
<br>
Deniz<br>
<br>
</blockquote>
<br></div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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