Hello,
On Mon, May 31, 2010 at 10:06 PM, tianyuan meng
<oceanrabbit.mty.gmail.com>wrote:
> Hi everyone,
> I've got the 1QS4.pdb file, downloaded from the pdb.org. I have already
> take
> out the information of chain B and I want to calculate the B-factor of it.
> I
> have written a shell script named "chainB.in" like this:
>
> trajin chainB.crd
> rms first out chainB.b :1-154.CA
> atomicfluct out chainB.bfactor .CA byatom bfactor
>
atomicfluct will give fluctuations of each atom throughout a trajectory.
The "bfactor" simply multiplies these fluctuations by the appropriate factor
to recover the "bfactor", which I understand as some metric of protein
flexibility. However, you have provided only a single structure. The
average fluctuation of each atom throughout the trajectory (of a single
frame) must be zero.
Note that this does NOT calculate the bfactor from crystallography data, it
calculates it from molecular dynamics data. Thus, if you really want to
compare a theoretical B-factor to an experimental one, you'll have to run MD
on the protein and post-process the trajectory with ptraj, using the average
structure as the reference (you'll need 2 scripts to do this: one to create
the average structure and the second to calculate the b-factors).
Good luck!
Jason
go
>
> But there's no result after running:*
>
> ptraj chainB.parm7 ptraj_chainB*
>
> I don't know what's wrong. Please give me some suggestion. Thank you in
> advance!
>
>
> Tianyuan
> --
> Bioengineering
> School of Life Science and Technology
> Xi'an Jiaotong University
>
> Mailbox 2046 No.28 Xianning West Road
> Xi'an, Shaanxi, 710049, P.R.China
>
> mty.007.stu.xjtu.edu.cn
> oceanrabbit.mty.gmail.com
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon May 31 2010 - 20:00:03 PDT
