[gmx-users] g_rms -bm

[Kowsar Bagherzadeh]

Dear Users, 
I am trying to analyze a ligand-protein simulation results. I read in the manual that using g_rms command with –bm option produces a matrix of average bond angle deviations. And only bonds between atoms in the comparison groups are considered.  Does it mean that it is for the bonds and their angles that are already in existence? (Not the ones that may be formed throughout simulation, I mean the ligand may for example interact with residues through H-bonds) .I have made a group in my index file named Active site (including only the active site residues), and I have a LIG group as well. If I choose these two groups for g_rms with this command:
g_rms –s *.tpr –f *.trr –o rmsd.xvg –bm bond.xpm –n *.ndx
Does it show me how the ligand affects the active site residues bond angles?
And one more question, how can I study the ligand orientation in the active site?
Sogol
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