[gmx-users] protein structural alignment

Ran Friedman r.friedman at bioc.unizh.ch
Mon Jul 23 14:37:09 CEST 2007

Dear Gromacs users,

I've written a program that runs the program "multiprot" on a gromacs
trajectory. multiprot is a program that does structural alignment of
proteins, i.e. it aligns two proteins based on structure and not
sequence. This can be useful e.g. when one compares a gromacs trajectory
to a protein that has a completely different sequence. It doesn't depend
on a similar index group as g_confrms. The output gives two xvg files,
one with the rmsd and one with the number of amino acids that were used
in the alignment.

Before submitting the program I'd be happy if interested people help me
by testing it.

To do this, you should first download and install do_multiprot:

and then contact me off list for the code or executable.


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