From: Xing (
Date: Tue Sep 15 2015 - 12:08:03 CDT

Dear John,

Thanks! I did use VMD 1.9.1. It's much better with VMD 1.9.2 now. :)
But there is still a problem in VMD 1.9.2. It seems that VMD will ignore the orders of atoms in the atom selection text, and I can only align the molecules properly after I updated the order of atoms
in the pdb files manually. Is there a way to force VMD to use the input order of atom section text instead of the internal orders in the pdb files in "atom pairing" (that is, 5-->7, 4-->6, 6-->4 in my
sample script) ?

Best wishes,

On 09/15/2015 11:58 AM, John Stone wrote:
> Hi,
> There was a limitation in older revs of VMD with regard to
> alignment of less than 4 atoms. I'm guessing that if you're
> having a problem that you must be runnig an older version of
> VMD and not VMD 1.9.2 or later.
> Cheers,
> John Stone
> On Tue, Sep 15, 2015 at 11:34:25AM -0400, Xing wrote:
>> 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
>> Xing