Hi Anupam , To me it seems that you have used the the wrong groups for the RMSD, you actually compare the protein to himself. Have a second look on at the group contact, you groups should be numbered 12 or higher.
cheers, Itamar -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut =========================================== | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@med.monash.edu.au ============================================ ----- Original Message ----- From: Anupam Nath Jha <anu...@mbu.iisc.ernet.in> Date: Sunday, May 9, 2010 3:48 pm Subject: [gmx-users] rmsd between different monomers To: gmx-users@gromacs.org > > Dear all > > I made an index file with 4 different groups for 4 different chains > (since my > protein is a tetramer) and then run > > g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out > > to get the rmsd between two different monomers from the same > structure,it asked me two different groups and I gave 0 and 1. > > The output file is like this > > # g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o New > # > # g_rms is part of G R O M A C S: > # > # Grunge ROck MAChoS > # > @ title "RMSD" > @ xaxis label "Time (ps)" > @ yaxis label "RMSD (nm)" > @TYPE xy > @ subtitle "C-alpha_chain2 after lsq fit to C-alpha_chain1" > 0.0000000 0.0000001 > > > so the rmsd = 0.0000001 > > whereas when I use online server it gives me 1.4. > > so what am I doing wrong? > > regrads > anupam > > > > -- > > Anupam Nath Jha > Ph. D. Student > Saraswathi Vishveshwara Lab > Molecular Biophysics Unit > IISc,Bangalore-560012 > Karnataka > Ph. no.-22932611 > > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before > posting!Please don't post (un)subscribe requests to the list. Use > the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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