Recalling with apologies the previous message.
Due to oversight I put in the 2nd script trajin average.pdb instead of reference average.pdb
Sorry
George
On Aug 23, 2012, at 2:28 PM, George Tzotzos wrote:
> 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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>
>
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Received on Thu Aug 23 2012 - 06:00:03 PDT
