AMBER Archive (1999)

Subject: Re: RMS fit summary

From: Carlos Simmerling (carlos_at_poblano.chem.sunysb.edu)
Date: Wed Oct 27 1999 - 14:29:16 CDT

Just a side note- our program MOIL-View can do RMSD
calculations, and make plots based on them, do clustering,
2D-RMSD, etc. The only restriction in doing the RMSD
is that the same number of atoms are chosen in each
molecule- they can be completely different molecules
with different numbers of atoms, and different atom sets
can be chosen for each molecule. Different atoms can be used
for fitting as compared to the actual RMSD (for example,
fit on the core and calculate the resulting deviation in a loop).
All of this can be done for static structures or over MD
trajectories. Prmtop files are not required (but can be used).

We're just finishing an updated user manual, but a recent
source code (and R10000 binary) and slightly older manual
can be found on the web page.

http://morita.chem.sunysb.edu/carlos/moil-view.html

The program is free and runs on SGI machines only.
Comments are welcome. 

--
===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor           Phone: (516) 632-1336
Department of Chemistry       Fax:   (516) 632-7960
SUNY at Stony Brook           Web:   http://morita.chem.sunysb.edu/carlos
Stony Brook, NY 11794-3400    E-mail: csimmerling_at_sbchem.sunysb.edu
===================================================================