Hi.<div>I have a small organic molecule that I processed with antechamber using the gaff forcefield and got a mol2 file. I want to get .gro and. itp files from this to use with GROMACS. So I tried to use the program "topolbuild version 1.2" from the GROMACS website.</div>
<div><br class="webkit-block-placeholder"></div><div>when I execute the command:</div><div>"topolbuild -dir ../ -ff gaff -n nameofmolecule -r SL -last 1241 -resnum 40"<br class="webkit-block-placeholder"></div><div>
I get this error message:</div><div><div>Fatal error.</div><div>Source code file: readmol2.c, line: 109</div><div>Atomic symbol cc in atom type not found.</div><div><br class="webkit-block-placeholder"></div><div>When I excecute the topolbuild above I use -dir ../ because that should take the program to the directory containing dat/antechamber and etc. which actually comes with the topolbuild 1.2 package</div>
<div><br class="webkit-block-placeholder"></div><div>I don't know what to do and I have tried searching this mailing list and google without sucess.</div><div><br class="webkit-block-placeholder"></div><div>Can someone please help me?</div>
<div><br class="webkit-block-placeholder"></div><div>Thanks.</div><div><br class="webkit-block-placeholder"></div></div>