Hi. 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.
when I execute the command: "topolbuild -dir ../ -ff gaff -n nameofmolecule -r SL -last 1241 -resnum 40" I get this error message: Fatal error. Source code file: readmol2.c, line: 109 Atomic symbol cc in atom type not found. 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 I don't know what to do and I have tried searching this mailing list and google without sucess. Can someone please help me? Thanks.
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