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
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
