VMD-L Mailing List

From: Ana Celia Araujo Vila Verde (avilaverde_at_engr.psu.edu)
Date: Tue Jan 31 2006 - 10:28:37 CST

Hi,

 

I'm using a script I found in the VMD website to compute the RMSD of a molecule relative to the same molecule at frame zero.

 

I want the output to go to a file, so I added the necessary commands. The file opens when I run the script but nothing gets written in it even though output does make it to the screen!

 

I'd really appreciate some help. Here's the script (the parts I added are between ######):

 

        # Prints the RMSD of the protein atoms between each \timestep

        # and the first \timestep for the given molecule id (default: top)

 

        proc print_rmsd_through_time {{mol top}} {

                # use frame 0 for the reference

                set reference [atomselect $mol "protein" frame 0]

                # the frame being compared

                set compare [atomselect $mol "protein"]

 

                set num_steps [molinfo $mol get numframes]

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

                set outFile RSMD_t0.rms

                set out [open $outFile w]

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

# Does this every 30 frames

                for {set frame 0} {$frame < $num_steps} {incr frame 30} {

                        # 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 "RMSD of $frame is $rmsd"

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

                        puts $out "RMSD of $frame is $rmsd"

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

                }

        }

 

 

 

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

_________________________________