I'm trying to calculate RMSF values of CA atoms for my trajectory and compare them to the corresponding ones of the X-ray structure.
I'm doing a rms fit according to the manual using the following input script
trajin my.mdcrd
rms first mass out rmsd.dat :1-123.CA
atomicfluct out bfactor.apf .CA byatom bfactor
The values obtained compare well to those of the X-ray structure.
If I do an rms fit to the average structure according to the script
trajin my.mdcrd
trajin average.pdb
rms reference mass out rmsd.dat :1-123.CA
atomicfluct out bfactor.apf .CA byatom bfactor
the values obtained are easily an order of magnitude higher.
There's obviously a glitch in the syntax of the script.
I'd be grateful for any suggestions
Best regards
George
On Aug 14, 2012, at 7:35 PM, Daniel Roe wrote:
> Hi,
>
> This is covered in the 'atomicfluct' section of the manual, although
> it is sort of buried near the end:
>
> "Note that RMS fitting is not done implicitly. If you want
> fluctuations without rotations or
> translations (for example to the average structure), perform an RMS
> fit to the average structure
> (best) or the first structure (see rmsd) prior to this calculation."
>
> On Tue, Aug 14, 2012 at 11:06 AM, Eliac Brown <eliacbrown.yahoo.com> wrote:
>> So, does it mean it is wrong to calculate the RMSF without prior RMS fitting step? in other words, are the calculated RMSF data without prior RMS fitting meaningless values?
>
> So, if you want to compare to B-factors you should RMS fit to an
> average structure prior to 'atomicfluct'.
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
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Received on Thu Aug 23 2012 - 05:30:02 PDT
