VMD-L Mailing List

From: Yixin Chen (yixin.chen1_at_ucdconnect.ie)
Date: Tue Oct 31 2023 - 10:55:22 CDT

Dear all,

I am a beginner of VMD and NAMD, I follow the NAMD TUTORIAL to study. I am
in the section of 1.8 Analysis of Water Sphere Equilibration
when I run the rmsd.tcl on Tk Console, there is an error:* bad for loop
variable*. to handle the error I use sudo dpkg-reconfigure dash and select
no to Change the default shell to bash.
After the chage, the error is also changed : *line 7: syntax error near
unexpected token `i' and line 7: `for {set i 1} {$i <= $nf} {incr i} {'*
Is there anyone who could help me to find the problem, thank you so much!

I use the Ubuntu 22.04.3 64 ; NAMD 3.0b4 linux x86_64; vmd-1.9.4a57
the rmsd.tcl file is get from required tutorial files witch download from
the the web.
the code is:

*set outfile [open rmsd.dat w]set nf [molinfo top get numframes]set frame0
[atomselect top "protein and backbone and noh" frame 0]set sel [atomselect
top "protein and backbone and noh"]# rmsd calculation loopfor { set i 1 } {
$i <= $nf } { incr i } {$sel frame $i$sel move [measure fit $sel
$frame0]puts $outfile "[measure rmsd $sel $frame0]"}close $outfile*

Best regards,
Yixin