<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt; font-family: "Times New Roman","serif";"><br></span></p><p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;">
<span style="font-size: 12pt; font-family: "Times New Roman","serif";">Hi gromacs users,</span></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><br><span style="font-size: 12pt; font-family: "Times New Roman","serif";"></span></p><p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;">
<span style="font-size: 12pt; font-family: "Times New Roman","serif";"></span><span style="font-size: 12pt; font-family: "Times New Roman","serif";" lang="X-NONE">I am using the gromacs 4.5.3 version.</span><span style="font-size: 12pt; font-family: "Times New Roman","serif";" lang="X-NONE"> 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.</span><span style="font-size: 12pt; font-family: "Times New Roman","serif";" lang="X-NONE"> <br>
</span></p><p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt; font-family: "Times New Roman","serif";" lang="X-NONE">Then, <span style="">when I used the following command in gromacs:</span></span></p>
<pre><span style="font-size: 12pt; font-family: "Times New Roman","serif";" lang="X-NONE"> pdb2gmx –f lipopepArgus.pdb<span style=""> </span>(GROMOS96 45a3 force field&spc type water model)</span></pre>
<pre><span style="font-size: 12pt; font-family: "Times New Roman","serif";" lang="X-NONE"> I got the following error message:</span></pre><pre><span style="font-size: 12pt; font-family: "Times New Roman","serif";" lang="X-NONE"> </span><span style="font-size: 12pt; line-height: 115%; font-family: "Times New Roman","serif";">Fatal error:</span></pre>
<p class="MsoNormal"><span style="font-size: 12pt; line-height: 115%; font-family: "Times New Roman","serif";">Residue 'DEF' not found in residue topology database</span></p>
<p class="MsoNormal"><span style="font-size: 12pt; line-height: 115%; font-family: "Times New Roman","serif";">For more information and tips for troubleshooting,
please check the GROMACS</span></p>
<p class="MsoNormal"><span style="font-size: 12pt; line-height: 115%; font-family: "Times New Roman","serif";">website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a></span></p>
<p class="MsoNormal"><span style="font-size: 12pt; line-height: 115%; font-family: "Times New Roman","serif";"> </span></p>
<p class="MsoNormal"><span style="font-size: 12pt; line-height: 115%; font-family: "Times New Roman","serif";">As far as I could understand, there is no problem
with the residues <span style=""> </span>but<span style=""> </span>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. <span style=""> </span>I thought<span style="">
</span>I should<span style=""> </span>r<tt><span style="line-height: 115%; font-family: "Times New Roman","serif";">ename
the pdb to the expected name given in the .rtp file of <span style=""> </span>the 45a3 force field for my lipopeptide. But I
could not find a parameterization for the <span style=""> </span>lauroic acid. In this case, what shoul I do?</span></tt></span></p>
<p class="MsoNormal"><tt><span style="font-size: 12pt; line-height: 115%; font-family: "Times New Roman","serif";"><br></span></tt></p><p class="MsoNormal"><tt><span style="font-size: 12pt; line-height: 115%; font-family: "Times New Roman","serif";">At the <span style=""> </span><a href="http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks">http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks</a>
page, I found;</span></tt></p><p class="MsoNormal"><tt><span style="font-size: 12pt; line-height: 115%; font-family: "Times New Roman","serif";"><br></span></tt></p>
<table class="MsoNormalTable" style="border-collapse: collapse; border: medium none;" border="1" cellpadding="0" cellspacing="0">
<tbody><tr style="">
<td style="width: 76.75pt; border: 1pt solid windowtext; padding: 0cm 5.4pt;" valign="top" width="102">
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><strong><span style="font-size: 12pt;">Abbrev.</span></strong><span style="font-size: 12pt; font-family: "Times New Roman","serif";"> <tt><span style="font-family: "Times New Roman","serif";"></span></tt></span></p>
</td>
<td style="width: 76.75pt; border-width: 1pt 1pt 1pt medium; border-style: solid solid solid none; border-color: windowtext windowtext windowtext -moz-use-text-color; padding: 0cm 5.4pt;" valign="top" width="102">
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><strong><span style="font-size: 12pt;">Source</span></strong><tt><span style="font-size: 12pt; font-family: "Times New Roman","serif";"></span></tt></p>
</td>
<td style="width: 76.75pt; border-width: 1pt 1pt 1pt medium; border-style: solid solid solid none; border-color: windowtext windowtext windowtext -moz-use-text-color; padding: 0cm 5.4pt;" valign="top" width="102">
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><strong><span style="font-size: 12pt;">2</span></strong><tt><span style="font-size: 12pt; font-family: "Times New Roman","serif";"></span></tt></p>
</td>
<td style="width: 76.75pt; border-width: 1pt 1pt 1pt medium; border-style: solid solid solid none; border-color: windowtext windowtext windowtext -moz-use-text-color; padding: 0cm 5.4pt;" valign="top" width="102">
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><strong><span style="font-size: 12pt;">Full Name</span></strong><tt><span style="font-size: 12pt; font-family: "Times New Roman","serif";"></span></tt></p>
</td>
<td style="width: 76.8pt; border-width: 1pt 1pt 1pt medium; border-style: solid solid solid none; border-color: windowtext windowtext windowtext -moz-use-text-color; padding: 0cm 5.4pt;" valign="top" width="102">
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><strong><span style="font-size: 12pt;">Formula</span></strong><tt><span style="font-size: 12pt; font-family: "Times New Roman","serif";"></span></tt></p>
</td>
<td style="width: 76.8pt; border-width: 1pt 1pt 1pt medium; border-style: solid solid solid none; border-color: windowtext windowtext windowtext -moz-use-text-color; padding: 0cm 5.4pt;" valign="top" width="102">
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><strong><span style="font-size: 12pt;">Specifics</span></strong><tt><span style="font-size: 12pt; font-family: "Times New Roman","serif";"></span></tt></p>
</td>
</tr>
<tr style="">
<td style="width: 76.75pt; border-width: medium 1pt 1pt; border-style: none solid solid; border-color: -moz-use-text-color windowtext windowtext; padding: 0cm 5.4pt;" valign="top" width="102">
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt; font-family: "Times New Roman","serif";">LAU
<tt><span style="font-family: "Times New Roman","serif";"></span></tt></span></p>
</td>
<td style="width: 76.75pt; border-width: medium 1pt 1pt medium; border-style: none solid solid none; border-color: -moz-use-text-color windowtext windowtext -moz-use-text-color; padding: 0cm 5.4pt;" valign="top" width="102">
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt; font-family: "Times New Roman","serif";">fa.itp<tt><span style="font-family: "Times New Roman","serif";"></span></tt></span></p>
</td>
<td style="width: 76.75pt; border-width: medium 1pt 1pt medium; border-style: none solid solid none; border-color: -moz-use-text-color windowtext windowtext -moz-use-text-color; padding: 0cm 5.4pt;" valign="top" width="102">
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt; font-family: "Times New Roman","serif";">O<tt><span style="font-family: "Times New Roman","serif";"></span></tt></span></p>
</td>
<td style="width: 76.75pt; border-width: medium 1pt 1pt medium; border-style: none solid solid none; border-color: -moz-use-text-color windowtext windowtext -moz-use-text-color; padding: 0cm 5.4pt;" valign="top" width="102">
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt; font-family: "Times New Roman","serif";">lauroic
acid<tt><span style="font-family: "Times New Roman","serif";"></span></tt></span></p>
</td>
<td style="width: 76.8pt; border-width: medium 1pt 1pt medium; border-style: none solid solid none; border-color: -moz-use-text-color windowtext windowtext -moz-use-text-color; padding: 0cm 5.4pt;" valign="top" width="102">
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt; font-family: "Times New Roman","serif";">C<sub>11</sub>H<sub>23</sub>COOH<tt><span style="font-family: "Times New Roman","serif";"></span></tt></span></p>
</td>
<td style="width: 76.8pt; border-width: medium 1pt 1pt medium; border-style: none solid solid none; border-color: -moz-use-text-color windowtext windowtext -moz-use-text-color; padding: 0cm 5.4pt;" valign="top" width="102">
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt; font-family: "Times New Roman","serif";">-<tt><span style="font-family: "Times New Roman","serif";"></span></tt></span></p>
</td>
</tr>
</tbody></table>
<p class="MsoNormal"><tt><span style="font-size: 12pt; line-height: 115%; font-family: "Times New Roman","serif";"> </span></tt></p>
<p class="MsoNormal"><tt><span style="font-size: 12pt; line-height: 115%; font-family: "Times New Roman","serif";">Does
using fa.itp file solve my problem? If yes, where can I get this file?</span></tt></p>
<pre><span style="font-size: 12pt; font-family: "Times New Roman","serif";" lang="X-NONE"><br>I would be so glad if you can help me solve this problem.<br>Thank you in advance,</span></pre><pre><span style="font-size: 12pt; font-family: "Times New Roman","serif";" lang="X-NONE">Deniz</span></pre>