From: Olya Kravchenko (okrav_at_ucdavis.edu)
Date: Mon Feb 14 2005 - 13:44:41 CST
Dear all! I have a question about rmsd calculation. When I try to run scripts
I have error that say:
-------------------------------------------
wrong # args: should be "proc name args body"
GET-RMSD) Defining structure and trajectories...
2chains.psf
2chains.pdb
min01.dcd
GET-RMSD) Computnig RMSD for entire protein...
2chains.psf 2chains.pdb min01.dcd
invalid command name "get_rmsd"
ERROR) No molecules loaded.
GET-RMSD) Computing RMSD for protein backbone...
2chains.psf 2chains.pdb min01.dcd
invalid command name "get_rmsd"
ERROR) No molecules loaded.
GET-RMSD) Computing RMSD for heme...
invalid command name "get_rmsd"
ERROR) No molecules loaded.
------------------------------------------------
I can't figure out what is wrong with description of get_rmsd process. I would
really appreciate your help.
Here are the scripts I use for this:
--------------------------------------------------------------------
proc get_rmsd {selstring outfile pdbfile psffile dcdfilelist}
{
# open output file (or quit if file exists already)
if {[file exists "${outfile}"]}{
puts "File \"${outfile}\" exists; delete it and re-run"
quit
}
set FIN [open "${putfile}"w]
#read crystallographic structure
puts "RMSD) Loading ${psffile}/${pdbfile}..."
mol load psf "${psffile}" pdb "${pdbfile}"
#set reference selections
puts "RMSD) Setting reference selection..."
set selref [atomselect top "$selstring"]
#analyze trajectories one by one
set netframenum 1
foreach dcdfile $dcdfilelist {
#load trajectory
puts -nonewhile "RMSD) Loading ${dcdfile}..."
mol new "$psffile" type {psf} first 0 last -1 step 1 waitfor all
set n [molinfo top get numframes]
puts -nonewline " read ${n} frames..."
#measure RMSD
for {set i 0} {$i < $n} {incr i} {
puts -nonewline $FIN "${netframenum}\t"
set selecomp [atomselect top "$selstring" frame $i]
set matrix [ measure fit $selcomp $selref]
$selcomp move $matrix
set r [ measure rmsd $selcomp $selref]
puts -nonewline $FIN "${r}\t"
puts $FIN ""
$selcomp delete
incr netframenum
}
mol delete top
puts " done."
}
close $FIN
}
---------------------------------------
and second (sources the first one):
--------------------------------
source rmsdByGroup.tcl
puts "GET-RMSD) Defining structure and trajectories..."
set dcdfilelist {}
set psffile "2chains.psf"
set pdbfile "2chains.pdb"
lappend dcdfilelist "min01.dcd"
lappend dcdfilelist "eq01.dcd"
lappend dcdfilelist "eq02.dcd"
lappend dcdfilelist "eq03.dcd"
puts "GET-RMSD) Computnig RMSD for entire protein..."
puts "$psffile $pdbfile $dcdfilelist"
get_rmsd "protein" "protein.dat" $pdbfile $psffile $dcdfilelist
mol delete all
puts "GET-RMSD) Computing RMSD for protein backbone..."
puts "$psffile $pdbfile $dcdfilelist"
get_rmsd "protein and backbone" "backbone.dat" $pdbfile $psffile $dcdfilelist
mol delete all
puts "GET-RMSD) Computing RMSD for heme..."
get_rmsd "noh and segid HEM" "heme.dat" $pdbfile $psffile $dcdfilelist
mol delete all
puts "GET-RMSD) COmputing RMSD for heme and environment..."
get_rmsd "noh and (segid HEM or protein and resid $hemenv)" "heme-env.dat"
$pdbfile $psffile $dcdfilelist
mol delete all
#end of file
------------------------------------
Thank you very much!
Olya
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