Hi,
On Mon, Feb 22, 2016 at 8:52 AM, Marc Zhang <marczhang_md.zoho.com> wrote:
>
> My question is why we should use "nofit" for the ligand but not the protein?
> If "nofit"is not specified, Is the RMSD for the ligand still legit or not?
> If not, why?
This has to do with the choice of reference frame. Typically you are
interested in the motion of the ligand with respect to the receptor -
therefore you perform an RMS-best-fit on the receptor (which becomes
your frame of reference) and then calculate the RMSD of the ligand
without further fitting (which would change your frame of reference).
If you were to specify:
rms reference mass out ligand_rmsd.dat :290
without the 'nofit' keyword you would be fitting on residue 290 as
well as calculating the RMSD, so the RMSD would now reflect internal
changes of residue 290.
Hopefully that answers your question.
-Dan
>
>
>
> Thanks a lot for your help!
>
>
>
> Cheers
>
> Marc
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Feb 22 2016 - 09:30:03 PST
