Subject: freeware for rmsd fit

From: Vlad Cojocaru <[email-masked]>
Date: Fri, 16 Aug 2002 11:30:09 +0200

Hi to all of you,
   I have a series of RNA mutants in which one base is mutated with a 
base analogue (for ex. 2AP). I ran MM on all of them and now I would 
like to fit the structures to the wild type rna structure by calculating 
rmsd. Since they are many structures, each of them has a different 
topology file. And now there comes my problem.
   I am using AMBER7 for calculations. When I try to fit the structures 
using CARNAL or PTRAJ it complains about the different topology files 
and it does not work. I tried with VMD but it seems to do something 
wrong because even though  the fit seems to be correct the rmsd values 
are not normal. So, my question is: does anyone know a freeware that can 
do what I am trying to do in a reliable way?
  Thanks a lot for any answers,
  Best regards,
vlad

-- 
Vlad Cojocaru 
Max Planck Institut for Biophysical Chemistry 
Deparment: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1389 
e-mail: [email-masked]