AMBER Archive (2002)

Subject: Re: CCL:freeware for RNA modeling on Linux (fwd)

From: amber_at_heimdal.compchem.ucsf.edu
Date: Tue Dec 03 2002 - 16:57:21 CST

---------- Forwarded message ----------
Date: Tue, 03 Dec 2002 13:49:12 -0500
From: Peter Gannett <pgannett_at_hsc.wvu.edu>
To: chemistry_at_ccl.net, amber_at_heimdal.compchem.ucsf.edu,
     Vlad.Cojocaru_at_mpi-bpc.mpg.de
Subject: Re: CCL:freeware for RNA modeling on Linux

Vlad:

I'm not sure what you mean...

If you mean building the RNA you might look at McSym ( http://www-lbit.iro.umontreal.ca/mcsym/ ) which is specifically designed for RNAs. Alternatively, NAB (http://www.scripps.edu/case/casegr-sh-2.2.html ) can also do what you want. Both are free.

If you want to do Molecular Mechanics/Dynamics, then NAMD ( http://www.ks.uiuc.edu/Research/namd/ ) can do the calculations and VMD ( http://www.ks.uiuc.edu/Research/vmd/ ) is a good viewer for the results. Both packages are free.

As an alternative to NAMD, amber ( http://www.amber.ucsf.edu/amber ) can do the MM/MD and is very inexpensive for an academic site.

Pete Gannett

>>> Vlad Cojocaru <Vlad.Cojocaru_at_mpi-bpc.mpg.de> 12/03/02 11:41AM >>>
Does anyone know a good freeware (or cheap software --academic use) for
RNA modeling.
I have an RNA stem and I would like to attach a loop to it.
Thanks alot,
vlad 

-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1389 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de 
home tel: ++49-551-9963204  

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