VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Sun Jan 23 2022 - 09:41:25 CST

Dear Kiana,
At least a couple of things that need to be fixed are (note that I use
backticks to enclose code excerpts below):
`veclenth` (sic) should be `veclength`
the `k` in the expression `"lindex ($coor1 k)"` is missing the `$` that
would indicate a variable reference
the lindex calls in that line should be `lindex $coor1 $k` , not `lindex
($coor1 k)`

In addition, even having fixed all of this, I suspect you're going to run
into a complaint about the use of the subtraction in that line because
you're trying to subtract two three-vectors; you should probably be using
`vecsub` instead of the `-` operator.

More generally, when confronted by a situation like this, I would highly
recommend beginning with a small piece of code that does your key
calculation and making sure that it works properly in isolation (eg, doing
a needed calculation on a single frame), and only then building up to the
larger script infrastructure. That way you (and anyone helping
troubleshoot) can focus better on where the problem is likely to be.
Best,
Peter

On Sun, Jan 23, 2022 at 7:20 AM Kiana Jahani <kiana.jahani_at_remove_yahoo.com>
wrote:

> Dear all,
> I have a dcd file and I want to calculate the distances between one atom
> and a series of atoms and select the minimum one in each frame. I wrote the
> following Tcl commands. But I got the following error in vmd:
> 'can't use non-numeric string as operand of "-" '
> (related to the expr command). I didnt realize what was the problem.
> Can anyone help me with that? I would appreciate it.
> Best,
> Kiana
>
> proc distance { seltext1 seltext2 f }
>
> set sel1 [atomselect top "seltext1"] ####select 150 atoms
> set sel2 [atomselect top "seltext2"] ####select one atom
>
> set nf [molinfo top get numframes]
>
> set outfile [open $f w] ###Open file specified by the variable f
>
> for {set i 0} {$i < $nf} {incr i} {
>
> puts "frame $i of $nf"
> $sel1 frame $i
> $sel2 frame $i
>
> set coor1 [$sel1 get {x y z}]
> set coor2 [$sel2 get {x y z}]
>
> set l2 { }
>
> for {set k 0} {$k < 150} {incr k} {
>
> lappend l2 [ veclenth [expr {"lindex ($coor1 k)" - "lindex ($coor2 0)" } ]
> ]
> }
>
> set min "$l2 0"
> for {set j 0} {$j < 165 } {incr j} {
> set t "$l2 j"
> if {$t < $min}
> set mindata($i.r) $t
> }
>
> puts $outfile "$i $mindata($i.r)"
>
> }
> close $outfile
>
>