[gmx-users] Metal Ion Position

[Justin A. Lemkul]

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

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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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