Dear all,
I'm trying to reproduce the step 2 of AMBER A1 tutorial with VMD (
http://ambermd.org/tutorials/advanced/tutorial1/section2.htm) 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. It seems that VMD cannot align a few atoms properly. My script is
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
It it adapted for protein alignment and works for many atoms... If there is nothing wrong in the script and VMD cannot do the alignment, what other software should I try?
Thanks very much and best wishes,
Xing
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Received on Tue Sep 15 2015 - 09:00:03 PDT
