Subject: RE: CCL:RMSD in Autodock

From: Robert Flight <[email-masked]>
Date: Fri, 30 Aug 2002 16:30:51 -0300

Hi Rowyna,

I dont know how the RMSD is calculated in Autodock3 exactly, but I might know 
how to get values from a different program to match those give by Autodock (or 
at least come close).  The program I use, MOE, assumes that all of the atoms 
are connected the same way and in the same order when doing the RMSD 
calculation.  After all of the processing to the Autodock pdbq file, all of 
the connectivity was messed up from the original structure.  I found if I took 
one of the docked results, and superposed the docked structure over the 
original reference structure, and then used the superposed structure from 
docking as your "new" reference; then I got RMSD values approaching those 
given by Autodock.  They're not the exact same, but pretty close.  This could 
be part of the problem you are haveing.

Hope this helps,

Robert

>===== Original Message From "[email-masked]" <[email-masked]> 
=====
>Hi CCLers,
>
>Does anybody know how the RMSD is calculated in Autodock3? I haven't been
>able to find out as of now. My initial thought was the heavy atoms of the
>docked conformations and reference structure were used. But when I use
>other programs like InsightII or VMD to calculate the RMSD, the values are
>quite different. Can I find out from the source code? I looked through but
>wasn't sure.
>
>Any suggestions/feedback would be appreciated. Thank you for your time.
>
>Sincerely,
>Rowyna
>
>
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********************************
Robert Flight
Masters Student
Department of Chemistry
University of New Brunswick
Fredericton, NB  Canada  E3B 6E2
e-mail: [email-masked] 
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