VMD-L Mailing List

From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Tue Sep 25 2012 - 11:56:05 CDT

Hi Brian, many thanks for your help.

I modify the scipt to:

proc myrmsd { frame } {
   global ref sel all
   $all move [measure fit $sel $ref]
   puts "$frame: [measure rmsd $sel $ref]"
 }
set mol [mol addfile CALDHmT178_wb_min4.coor type pdb waitfor all]
set all [atomselect $mol all]
set ref [atomselect $mol "name CA" frame 0]
set sel [atomselect $mol "name CA"]
set outfile [open rmsd.dat w];
puts $outfile "[measure rmsd $sel $ref]"
bigdcd myrmsd dcd CALDHmT178_wb_eq5.dcd
bigdcd_wait
close $outfile

But it still does not work.
Maybe is because I am not sure about how to "Make it global"

Sorry about the basic question, but I am not familiar with tcl scripts. I google it, but no clues about what to do...

Any advice?

Regards,

Flavio

--- On Tue, 9/25/12, Bennion, Brian <Bennion1_at_llnl.gov> wrote:

> From: Bennion, Brian <Bennion1_at_llnl.gov>
> Subject: RE: vmd-l: Big DCD file help
> To: "flavio seixas" <oivalf_nix_at_yahoo.com>, "VMD List" <vmd-l_at_ks.uiuc.edu>
> Date: Tuesday, September 25, 2012, 5:43 PM
>
> Not tested
>
> Open a file
> Set fh1 [open "rmsd.plt" w]
> Make it global and in the proc add
>
> puts $fh1 "$frame: [measure rmsd $sel $ref]"
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu
> [mailto:owner-vmd-l_at_ks.uiuc.edu]
> On Behalf Of flavio seixas
> Sent: Tuesday, September 25, 2012 8:16 AM
> To: VMD List
> Subject: vmd-l: Big DCD file help
>
> Hi,
>
> I am trying to calculate rmsd from my dcd files. The namd
> rmsd tcl script is working fine. Unfortunately the values
> appears listed in tk window and can not be copied at all.
> Is possible to put the rmsd values in a file?
>
> This is my script:
>
>
> proc myrmsd { frame } {
>    global ref sel all
>    $all move [measure fit $sel $ref]
>    puts "$frame: [measure rmsd $sel $ref]"
> }
> set mol [mol addfile CALDHmT178_wb_min4.pdb type pdb waitfor
> all] set all [atomselect $mol all] set ref [atomselect $mol
> "name CA" frame 0] set sel [atomselect $mol "name CA"]
> bigdcd myrmsd dcd CALDHmT178_wb_eq5.dcd bigdcd_wait
>
>
>