[gmx-users] RMSD Calculation

Alper Kucukural alper at mindsventure.com
Mon Dec 26 15:43:25 CET 2005

I have just installed Gromacs-3.3 successfully. I want to calculate RMSD value between two pdb files. I already wrote a program to select some parts in pdb files. For example I select 1,6,7,15... CA Atoms in first pdb file and 4,8,9,10... CA Atoms in second pdb file. Ofcourse the list size is equal and I want to superimpose these proteins and find RMSD value. Is it possible to send me an example how I can do this with Gromacs-3.3.
Thanks in advance...

Alper Kucukural
Phd in Biological Sciences and Bioengineering
Sabanci University
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