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From: Mustafa Tekpinar (tekpinar_at_buffalo.edu)
Date: Tue Jan 31 2012 - 13:48:40 CST
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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)
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
- Next message: John Stone: "Re: NewRibbons/NewCartoon problem due to missing CUDA ?"
- Previous message: Ajasja Ljubetič: "Re: NewRibbons/NewCartoon problem due to missing CUDA ?"
- Next in thread: Axel Kohlmeyer: "Re: Rmsd script with arguments"
- Reply: Axel Kohlmeyer: "Re: Rmsd script with arguments"
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