I am performing grompp for md simulation after position restrained MD. Before final md simulation by grompp I have made pr.ndx file and did necessary corrections in it to insert added Na+ to be counted properly. But after running the following command -
grompp -f md.mdp -c pr.gro -p scr8.top -o md.tpr the output came: Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'NA+' turning all bonds into constraints... processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Analysing residue names: Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat There are: 2670 OTHER residues There are: 28 PROTEIN residues There are: 0 DNA residues Analysing Protein... Analysing Other... ------------------------------------------------------- Program grompp, VERSION 4.0.2 Source code file: readir.c, line: 1050 Fatal error: 2 atoms are not part of any of the T-Coupling groups ------------------------------------------------------- Even the .top file was also modified to include extra Na+. Please help to get a solution. Chitrita..
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