[Chimera-users] RMSD i.b and RMSD u.b

Elaine Meng meng at cgl.ucsf.edu
Mon May 20 09:41:17 PDT 2013


Please send Chimera questions to chimera-users at cgl.ucsf.edu instead of just my address.

The RMSD lb (lower bound) and RMSD ub (upper bound) of a docked ligand are calculated by AutoDock Vina and are described in the manual for that program:

<http://vina.scripps.edu/manual.html>

(go to that page and search for "RMSD")

I believe they just indicate how similar each position is to the best-scoring position found.  
I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 20, 2013, at 6:10 AM, Muhammad ALi <muh.ali741 at yahoo.com> wrote:

> AOA
> 
> sir
> when I check my result with ViewDock their are two RMSD values i.e    RMSD  i.b   and   RMSD u.b    plz tell me about them.....




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