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<DIV>Hi everyone!</DIV>
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<DIV>I added a residue on the gromacs 4.5.3 I have. I followed the instructions as indicated in the "Adding A Residue to a Force Field" with this link <U>http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field?highlight=adding+residue</U>. I added the residue to residuetypes.dat and indicated it as a carbohydrate. The topology in fact was able to write it down as a carbohydrate. </DIV>
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<DIV>Generating a topology went well with pdb2gmx, editconf, genbox, energy minimization. However, I encountered the following error when I was about to do an NVT equilibration.</DIV>
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<DIV>Program grompp, VERSION 4.5.3</DIV>
<DIV>Source code file: readir.c, line: 1316</DIV>
<DIV>Fatal error:</DIV>
<DIV>Group protein not found in indexfile.</DIV>
<DIV>Maybe you have non-default groups in your mdp file, while not using the '-n' option of grompp.</DIV>
<DIV>In that case use the '-n'option.</DIV>
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<DIV>In response, I created an index file using make_ndx. The index file was able to generate correctly the molecule indices and identified it correctly as indicated in the residuetypes.dat and carbohydrate.rtp </DIV>
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<DIV>And then I tried (again) the following command:</DIV>
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<DIV>$ grompp -f nvt.mdp -c molecule.gro -n index.ndx -p topol.top -o nvt.tpr. </DIV>
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<DIV>It still generates the same error as above. Please help</DIV></FONT></td></tr></table>