From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Sun Jul 26 2009 - 05:39:19 CDT

actually, rmsf over CA atoms can be done in vmd Tk console:

#load trajectory
mol load psf protein.psf
mol addfile protein.dcd waitfor all
#select CA atoms
set ca [atomselect top "protein and name CA"]
set rmsf [measure rmsf $ca]
set outfile [open "rmsfCA.txt" w]
foreach x $rmsf {
  puts $outfile $x
}
close $outfile

On Fri, Jul 24, 2009 at 12:15 PM, Roman Petrenko<rpetrenko_at_gmail.com> wrote:
> oh! you want per residue, sorry. have a look at this:
>
> http://195.130.120.154/wiki/index.php/Eucb:rmsf
>
> it is very easy to download and install
> http://195.130.120.154/eucb
>
>
>
> On Fri, Jul 24, 2009 at 10:00 AM, Roman Petrenko<rpetrenko_at_gmail.com> wrote:
>> last section on this page
>> http://www.ks.uiuc.edu/Research/vmd/current/ug/node187.html
>>
>> On Fri, Jul 24, 2009 at 9:06 AM, Dawn<dawn1313_at_gmail.com> wrote:
>>> Hi,
>>>
>>> I have the CHARMM MD trajectory. I want to calculate the average RMSD over
>>> all snapshots for each residue. Would you please tell me where I can get the
>>> script?
>>>
>>> Thanks a lot!
>>>
>>> Dawn
>>
>>
>>
>> --
>> Roman Petrenko
>> Physics Department
>> University of Cincinnati
>>
>
>
>
> --
> Roman Petrenko
> Physics Department
> University of Cincinnati
>

-- 
Roman Petrenko
Physics Department
University of Cincinnati