When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it is showing the following options: 0 System : 18379 atoms 1 Protein : 11739 atoms 2 Protein-H : 9135 atoms 3 C-alpha : 1173 atoms 4 Backbone : 3519 atoms 5 MainChain : 4693 atoms 6 MainChain+Cb : 5773 atoms 7 MainChain+H : 5842 atoms 8 SideChain : 5897 atoms 9 SideChain-H : 4442 atoms 10 Prot-Masses : 11739 atoms 11 non-Protein : 6640 atoms 12 Water : 6636 atoms 13 SOL : 6636 atoms 14 non-Water : 11743 atoms 15 Ion : 4 atoms 16 CL : 4 atoms 17 Water_and_ions : 6640 atoms
for my work, I used 16|13 then 1|11.lastly I saved it using 'q'.But there is no option for DPPC (as given in tutorial we have to merge protein with DPPC).After runing the command (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),it is showing error: Group DPPC 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. To troubleshoot the error,I have kept one more group in index.ndx file with number of atoms which I found from dppc.itp file(at the end of file) like this [DPPC] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 Again after running the grompp command (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),I am getting the following error: Atom 1 in multiple T-Coupling groups (1 and 2). Please suggest me the reason as well as solution for this problem.
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