VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Fri Jan 25 2008 - 14:14:53 CST

Thanks to John Stone's help, I got my batch angle measuring script working. It now looks like this:

mol load pdb tcnw.pdb dcd h5cnw.dcd
set outf [open h5ctheta.txt w]
set sel [atomselect top all]
set nf [molinfo top get numframes]
for {set i 0} {$i < $nf} {incr i} {
 set ang [ measure angle {22548 22527 22500} frame $i]
 puts $outf "$i $ang"
}
close $outf

where the atom numbers were identified from tcnw.pdb.

I invoke it like this:

/share/apps/vmd_1.8.6/vmd -dispdev text -eofexit thet1.log

My full dcd file contains 37429 frames & 1470 residues. This script works great with a test dcd I made by using catdcd to write every 10th frame, and it only takes 1 to 2 minutes to execute.

I had left the full problem to run overnight & this morning it was still going - seemed to be hung up, so I put it out of its misery. I'm trying the full run again, having convinced myself the script ought to work, & it looks like it's hanging again. Am I
running up against some allocation limit with the full dcd file?

Thanks again!
Irene Newhouse
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