Thank you! I changed the residue names in the .pdb file to LYQ and GLQ
LYQ NZ 1 GLQ C 1 0.13 LYQ GLQ pdb2gmx -f ubc7_94_t48_newgmx1.pdb -o processed.gro -water tip3p -chainsep interactive -ignh -rtpres Program pdb2gmx, VERSION 4.5.4 Source code file: resall.c, line: 581 Fatal error: Residue 'LYQ' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- I checked http://www.gromacs.org/Documentation/File_Formats/Topology_File But as you see from the previous mail, I included LYQ and GLQ to the force field. Maybe I missed something? -- Sincerely, Yulian Gavrilov
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