Dear Sir , I used your CG parameters and gromacs V3.3 to simulate protein aggregation. And my command is : grompp_mpi_d -np 2 -f aggre.mdp -c aggre.gro -p aggre.top -o aggre.trp The error message is : double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K renumbering atomtypes... converting bonded parameters... # BONDS: 1935 # G96ANGLES: 2565 # IDIHS: 225 # CONSTR: 900 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file /opt/gromacs//share/gromacs/top/aminoacids.dat There are: 76048 OTHER residues There are: 1170 PROTEIN residues There are: 0 DNA residues Analysing Protein... Analysing Other...
------------------------------------------------------- Program grompp_mpi_d, VERSION 3.3.3 Source code file: readir.c, line: 798 Fatal error: Group Protein1 not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. But I tried your example case "A toy peptide in water" , I still got the same error . My command is : 1.grompp_mpi_d -np 2 -f toypeptide.mdp -p toypeptide.top -c toypeptide.gro -n index.ndx -o toypeptide.tpr 2.grompp_mpi_d -np 2 -f toypeptide.mdp -p toypeptide.top -c toypeptide.gro -o toypeptide.tpr ____________________________________________________________________________________ index.ndx : [ prot_sort ] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 -------------------------------------------------------------------------------------------------------------------------------------------------------- The error message : Walking down the molecule graph to make shake-blocks initialising group options... processing index file... ------------------------------------------------------- Program grompp_mpi_d, VERSION 3.3.3 Source code file: readir.c, line: 798 Fatal error: Group TOYPEP not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. Sir, could you tell me how to fix the problem? By the way, I test other cases in your website and I didn't get any error message . Best regards Wang Yeng-tseng
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