If you view your mdcrd as a movie e.g. using VMD, you should be
able to see what is going on. If indeed a molecule or your whole
system is being translated due to iwrap=1, then you can use ptraj
to untranslate it using I believe the center cmd.
Sindrila Dutta banik <sindrila.duttabanik.yahoo.com> 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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Received on Mon Jan 16 2012 - 12:00:03 PST
