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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Shima,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">It seems like this residue is not parameterized for the force field you want to use. Maybe check
<a href="http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks">
http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks</a> if you can find it under a different name. If not, have a look at
<a href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field">
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a>.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Felix<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="DE" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Von:</span></b><span lang="DE" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]
<b>Im Auftrag von </b>Shima Arasteh<br>
<b>Gesendet:</b> Donnerstag, 12. April 2012 09:43<br>
<b>An:</b> Discussion list for GROMACS users<br>
<b>Betreff:</b> [gmx-users] Residue 'FOR' not found in residue topology database<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Arial","sans-serif";color:black">Dear Gromacs friends,<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Arial","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Arial","sans-serif";color:black">I attached my .pdb file in this message, as you see, I have formyl residue in it. I'd like to get a .gro output of it by using this commands, but getting
the fatal error:<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Arial","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Arial","sans-serif";color:black"># pdb2gmx -f glc.pdb -o glc.gro -ignh -ter -water spc
<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Arial","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Arial","sans-serif";color:black">Fatal error:<br>
Residue 'FOR' not found in residue topology database<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Arial","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Arial","sans-serif";color:black">How can I solve this problem?
<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Arial","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Arial","sans-serif";color:black">Thanks ,<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Arial","sans-serif";color:black">Shima<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Arial","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Arial","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Arial","sans-serif";color:black"><o:p> </o:p></span></p>
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