When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it is showing the following options:<br> 0 System : 18379 atoms<br> 1 Protein : 11739 atoms<br> 2 Protein-H : 9135 atoms<br>
3 C-alpha : 1173 atoms<br> 4 Backbone : 3519 atoms<br> 5 MainChain : 4693 atoms<br> 6 MainChain+Cb : 5773 atoms<br> 7 MainChain+H : 5842 atoms<br> 8 SideChain : 5897 atoms<br>
9 SideChain-H : 4442 atoms<br> 10 Prot-Masses : 11739 atoms<br> 11 non-Protein : 6640 atoms<br> 12 Water : 6636 atoms<br> 13 SOL : 6636 atoms<br> 14 non-Water : 11743 atoms<br>
15 Ion : 4 atoms<br> 16 CL : 4 atoms<br> 17 Water_and_ions : 6640 atoms<br><br>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:<br>
<br>Group DPPC not found in indexfile.<br>Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp.<br>In that case use the '-n' option.<br><br>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<br>
<br>[DPPC]<br>1 2 3 4 5 6 7 8 9 10 11 12 13 14 15<br>16 17 18 19 20 21 22 23 24 25 26 27 28 29 30<br>31 32 33 34 35 36 37 38 39 40 41 42 43 44 45<br>
46 47 48 49 50<br><br>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:<br><br>Atom 1 in multiple T-Coupling groups (1 and 2).<br>
<br>Please suggest me the reason as well as solution for this problem.<br>