Thank you Daniel. One additional question. I've checked a number of definitions of B-factors and none of the ones that I've seen included the /3 factor. Any suggestions of how is this factored in would be most useful.
George
On May 27, 2013, at 9:13 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> It should read Ang^2*(8/3)*PI^2.
>
> Note that if you haven't already I recommend you upgrade to the latest
> AmberTools version (13).
>
> -Dan
>
> On Mon, May 27, 2013 at 11:34 AM, George Tzotzos <gtzotzos.me.com> wrote:
>> I'm quoting from the AmberTools 1.5 Manual p. 114
>>
>> If the keyword “bfactor” is specified, the data is output as B-factors rather than atomic positional fluctuations (which simply means multiplying the squared fluctuations by 8/3 π2). The data is dumped into two columns (n and value) where n goes from 1 to the number of atoms or groups specified and the value is the appropriate RMSF (Å) or B-factor (Å2 × 8/3 π ).
>>
>> My question is whether B-factor units are given in Å2 × (8/3 π) or Å2 × (8/3 π2)?
>>
>> Regards
>>
>> George
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>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
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Received on Mon May 27 2013 - 12:30:03 PDT
