VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jan 31 2012 - 15:55:06 CST

On Tue, Jan 31, 2012 at 2:48 PM, Mustafa Tekpinar <tekpinar_at_buffalo.edu> wrote:
> Hi,
> I am trying to calculate rmsd of a pdb file vs each frame of a trajectory
> and write results to a file. However, it  doesn't work with arguments
> properly. The error and the script is below:
>
> can't read "pdb_name": no such variable
> can't read "target_pdb": no such variable
> Cannot find molecule 0 in atomselect's 'molId'
> can't read "pdb_name": no such variable
> can't read "data_file_name": no such variable
> can't read "traj_psf": no such variable
> can't read "traj_dcd": no such variable
> Cannot find molecule 1 in atomselect's 'molId'
> molinfo: get: no molecule exists with id 1
> can't read "num_steps": no such variable
> can't read "file": no such variable
> can't read "compare": no such variable
> can't read "reference": no such variable
> ERROR) No molecules loaded.
> Info) VMD for LINUXAMD64, version 1.8.6 (April 6, 2007)

don't you think it is time to upgrade to a more recent
version of VMD after almost five years?

axel.

> Info) Exiting normally.
>
>
> //===========================================================================================================
> if { $argc != 3 }
>         puts "Usage: vmd -dispdev text -e rmsd_traj.tcl -args pdb_name(W/out
> extension) trj.psf trj.dcd"
> } else {
>     set pdb_name   [lindex $argv 0]
>     puts "[lindex $argv 0]"
>     set traj_psf   [lindex $argv 1]
>     puts "[lindex $argv 1]"
>     set traj_dcd   [lindex $argv 2]
>     puts "[lindex $argv 2]"
> }
>
> #set pdb_name
> 1yzi
> set target_pdb ${pdb_name}.pdb
>
> mol new ${target_pdb}
> set reference [atomselect 0 "name CA"]
>
> set data_file_name rmsd_${pdb_name}_to_trj_test.dat
> set file [open "$data_file_name" w]
>
> mol new ${traj_psf} waitfor all
> mol addfile ${traj_dcd} waitfor all
>
> # the frame being
> compared
> set compare [atomselect 1 "name CA"]
>
> set num_steps [molinfo 1 get numframes]
> for {set frame 0} {$frame < $num_steps} {incr frame} {
>
>     # get the correct
> frame
>     $compare frame $frame
>
>     # compute the
> transformation
>
>     set trans_mat [measure fit $compare $reference]
>
>     # do the
> alignment
>     $compare move $trans_mat
>
>     # compute the
> RMSD
>     set rmsd [measure rmsd $compare $reference]
>
>     # print the
> RMSD
>     puts $file "$frame \t$rmsd"
> }
> close $file
> $compare delete
> $reference delete
> mol delete all
> exit
> //===========================================================================================================
> Mustafa Tekpinar
>
> Department of Physics
> SUNY at Buffalo,
> Buffalo, NY
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.