Hello, I want to analyze the deuterium order parameter of a system contains DPPC, sphingomyelin(SM) and cholesterol(CHOL) and water(SOL). I read from the prevous mail that I have to make index file for sn1 and sn2. Now, my first question is what the meaning of sn1 and sn2 is. How can I assign from the .pdb file of the total system. make_ndx -f dppc20-sm20-cholesterol20-water200tolerance3-bilayer50x50x54.pdb 0 System : 3180 atoms 1 DPP : 1000 atoms 2 SM : 1000 atoms 3 CHOL : 580 atoms 4 SOL : 600 atoms
nr : group ! 'name' nr name 'splitch' nr Enter: list groups 'a': atom & 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr 'splitat' nr 'h': help 'r': residue 'res' nr 'chain' char "name": group 'case': case sensitive 'q': save and quit I understand that after giving the make_ndx command, I have to use above of these command ( a, t r ). But what are the full command so that I can make clear nice index file for the analysis of deuterium order parameter. In my case, for the the numbering of DPPC is like that : two tail starts from C13 to C31 and C13 to C50; SM is like that: two tails starts from C13 to C32 and C13 to C50; CHOL is like that : OH group is at 6 & 7and small tail comes from C21 to C29. Can you write the full command so that I can clearly understand clearly. Because, the next step I know that is g_order -f name.trr -n index.ndx -s topol.tpr -od Please, can you give the answer for me ? Sincerely, Anirban
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