VMD-L Mailing List
From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Fri Aug 10 2012 - 09:17:57 CDT
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Hi Axel and Yves,
Thank you for your suggestion.
My intention is to observe which residues are more flexible within the last 1000ps of dynamics (equilibrated stage).
To do that, I am trying to create a *.dat file in order to generate a plot of B-factor (or rmsf) at Y coordinates against residue number (at X coordinates).
Searching vmd-list, i found this script:
set outfile [open rmsf.dat w]
set sel [atomselect top "name CA"]
puts $outfile "[measure rmsf $sel first 4021 last 5020 step 1]"
close $outfile
My questions are:
1) The output of the above script displays a single column with 100 numbers. My protein has 233 residues, and I was expecting 233 numbers in the output file. Obviously I assume that the output file does not contain my desired information! What is missing?
2) I am not an expert in tcl script, but I wonder if I need to align the protein with the trajectory first? If it is correct, how is the command line(s) that I must put in the script?
3) Or, may I firstly align the protein using "RMSD Trajectory Tool" and then run the script?
Thanks for any help.
Flavio
--- On Thu, 8/9/12, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> Subject: Re: vmd-l: B-factor plugin
> To: "Wang Yi" <dexterwy_at_gmail.com>
> Cc: "flavio seixas" <oivalf_nix_at_yahoo.com>, "VMD List" <vmd-l_at_ks.uiuc.edu>
> Date: Thursday, August 9, 2012, 9:50 PM
> On Thu, Aug 9, 2012 at 10:00 PM, Wang
> Yi <dexterwy_at_gmail.com>
> wrote:
> > set allatoms [atomselect top all]
> > $allatoms get beta
> >
> > You need to read the online manual for VMD keywords.
> > By the way, why extracting B-factors from trajectory?
> Is there any thing
> > during your simulation will change the B-factor?
>
> i suppose the question would work the other way around:
> provided you do an MD of a crystal, can you measure
> the mobility of atoms around their centers and translate
> that into an approximation of the beta factor?
>
> i don't know of anything that would be a direct
> translation,
> but the calculation of RMSF values with "measure rmsf"
> might be a starting point.
>
> cheers,
> axel.
>
> >
> > ___________________________
> >
> > Yi (Yves) Wang
> > Duke University
> >
> >
> >
> >
> >
> > On 2012-8-9, at 下午3:13, flavio seixas wrote:
> >
> > Hi all,
> >
> > Anyone knows a tcl script to extract the B-factors
> values of protein
> > residues (or atoms) from namd trajectory file?
> >
> > I´ll be thankful for any help.
> >
> > regards,
> >
> > flavio
> >
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste.
> Italy.
>
>
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