simon sham wrote:
Hi,
I have a question on how to calculate the metal ion position in a
protein in a simulation.
To be more more specific, I would like to make sure the metal ion stay
in the binding site throughout the simulation, and not sure which
analysis function to use.
I have tried g_rms, and did not work. I'd appreciate your help.
g_traj can print coordinates, and g_dist can give distances relative to amino
acids in the protein (with custom index groups). Otherwise, g_rms can be
useful, if used properly (i.e. fit to the protein and measure the ion's RMSD).
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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