VMD-L Mailing List

From: Ana Celia Araujo Vila Verde (avilaverde_at_engr.psu.edu)
Date: Thu Feb 16 2006 - 13:31:28 CST

Dear all,

 

Based on the script to obtain the RMSD of one molecule relative to the same molecule at time 0, which can be found on the VMD manual, I built a very similar one to calculate the RMSD just for certain selections of the protein (see below signature). My problem is that if I do

 

selection "sheet protein backbone", the RMSD for sheet is OK but for protein and for backbone is wrong (I think).

 

If I take the exact same procedure and simply change to

 

selection " protein "

 

 and then to

 

selection "backbone ",

 

I get different values for their respective RMSD! This leads me to think that the RMSD I get for protein and for backbone when I use """ selection "sheet protein backbone" """ is incorrect.

 

Could anyone shine some light on this? Clearly I'm doing something wrong, but I looked at the code for hours and could not find it.

 

Thanks Ana

 

_________________________________

Ana Célia Araújo Vila Verde

Penn State University

Department of Chemical Engineering

Fenske Laboratory
University Park, PA 16802

USA

 

Phone: +(1) (814) 863-2879
Fax: +(1) (814) 865-7846

avilaverde_at_engr.psu.edu

_________________________________

 

To execute I type vmd -dispdev text -e nameOfFile.tcl on the unix command line.

 

proc print_rmsd0_through_time {{mol top}} {

 

##################################

        set selection "sheet protein backbone" ;# the RMSD calculation is done for the elements of this list

#################################

        set refFrame 0 ;# the RMDS is calculated against this reference

        set incrm 1; # the comparison is done every incrm number of frames

        set durTimestep 0.000002; # duration of the timestep in the simulation, in nanoseconds

        set stepsFrame 500; # number of timesteps in each frame in *dcd fil

#-----------------------------------------------------------------------------

 

        foreach sel $selection {

                set outFile try21RMSD_${sel}_refFrame${refFrame}.txt; # result goes to this file

                set out [open $outFile w]

                puts $out "computing RMSD for all sheets using frame $refFrame as reference"

                puts $out "time (ns) RMSD (angstrom)"

 

                set reference [atomselect $mol "protein and $sel" frame $refFrame]

                # the frame being compared

                set compare [atomselect $mol "protein and $sel"]

 

                set num_steps [molinfo $mol get numframes]

# Does comparison every incrm 30 frames

                for {set frme $refFrame} {$frme <= $num_steps} {incr frme $incrm} {

                        # get the correct frame

                        $compare frame $frme

 

                        # 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 "RMSD of $frame is $rmsd"

                        set time [expr {$frme*$stepsFrame*$durTimestep}]

                        puts $out "$time $rmsd"

                }

        close $out

        $compare delete

        unset trans_mat

        unset rmsd

        unset reference

        unset num_steps

        }

}

# Call procedure

print_rmsd0_through_time

#

quit