From: Xing (
Date: Tue Sep 15 2015 - 10:34:25 CDT

Dear all,

I'm trying to reproduce the step 2 of AMBER A1 tutorial with VMD. ( because Sirius is no longer available. However VMD can never
superposition the "anchor atoms" and the two structures (linker and dye) cannot be aligned as shown in the tutorial. I tried to increase the number of anchor atoms and the problem still exists. The
script is as

set anc_linker [atomselect 4 "index 5 4 6"]
set anc_dye [atomselect 3 "index 7 6 4"]
set linker_to_dye [measure fit $anc_linker $anc_dye]
set all_linker [atomselect 4 "all"]
$all_linker move $linker_to_dye

Is there something wrong in the script or VMD just cannot align only a few atoms?

Sincerely yours