VMD-L Mailing List

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Wed Aug 14 2002 - 10:46:48 CDT

I noticed a problem with the rmsd calculation. I am using 1.7.1 version.
If I am calculating the rmsd of two structures using the following script

logfile vmd.log
mol load pdb rna_ion_wat_mdeq0.pdb
mol load pdb rna_ion_wat_0.pdb
set sel1 [atomselect 0 "resid 1 to 17"]
set sel2 [atomselect 1 "resid 1 to 17"]
measure rmsd $sel1 $sel2
set tm [measure fit $sel1 $sel2]
set move_sel [atomselect 0 "all"]
$move_sel move $tm
#mol modselect 0 0 {resid 1 to 17}
#mol modselect 0 1 {resid 1 to 17}

it gives for the 2 structures that are almost perfectly overlaid a value
of 3.7... obviously abnormal since I calculated the same thing with many
other programs and the value is 0.267. I must say that this script is
working sometimes pretty fine with other structures. Does anybody have
any ideea what might happen here?
Thanks a lot,
vlad 

-- 
Vlad Cojocaru 
Max Planck Institut for Biophysical Chemistry 
Deparment: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1389 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de