Dear Sindrila
Please try to look at previous answers to this same question in the
amber mail list, there are tons of those available. Google it if needed,
and perhaps more importantly, read the manual. Page 115 in the
Ambertools manual says
"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 rms) prior to this calculation."
Adrian
On 1/16/12 12:43 PM, Sindrila Dutta banik wrote:
> How could I understand the translation of the system across the box. If I want to ignore the translational motion of the protein and compute the B factor then how to do this. Shall I have to change the script file which I am using now. A present I use the following script file
>
> trajin MD.mdcrd
> atomfluc out BF.rms byatom .CA bfactor
>
> With best regards
>
> From: Bill Ross<ross.cgl.ucsf.EDU>
> To: amber.ambermd.org; sindrila.duttabanik.yahoo.com
> Sent: Sunday, 15 January 2012 12:55 AM
> Subject: Re: [AMBER] Question related to the B factor
>
> Maybe the molecule was translated across the box for 2900 ps to 3000 ps?
> Have you watched the trajectory to see what the anomaly might be?
>
> Bill
>
> Sindrila Dutta banik<sindrila.duttabanik.yahoo.com> wrote:
>
>> Dear all
>>
>>
>> I have generated a trajectory of a protein system for 3 ns . Now I am comparing the B factor for the alpha carbon atoms computed from my trajectory with the experimental B factor. The result does not mach exactly with the experimental value.
>>
>> A surprising difference is observed for the trajectory from 2900 ps to 3000 ps. The B factor for this range (2900 ps to 3000 ps that is interval of 100 ps) is more than 10000000000 for all residues. But for other ranges the value does not differ so much. What could be the possible reason for this? Shall I done any mistake?
>>
>> I analyse the geometry of the system at 2900 ps and 3000 ps. The analysis shows a little difference in the geometry in two cases.
>>
>> With best regards
>> Sindrila
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--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Mon Jan 16 2012 - 10:00:04 PST
