[gmx-users] RMSD Calculation

[Justin A. Lemkul]

Nancy wrote:
> Hi All,
> 
> I need to determine the RMSD of a small molecule cocrystallized ligand, 
> against a large number of predicted docked conformations.  Please let me 
> know what is the best method for doing this.
> 

I answered this yesterday:

http://lists.gromacs.org/pipermail/gmx-users/2011-March/059697.html

If there's some reason you can't get that to work, then don't simply re-post the 
same original question.  Iterative calls to g_rms are quite straightforward to 
script.

-Justin

> Thank you very much,
> Nancy
> 

-- 
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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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