implementing RBCG

From: Michael Zimmermann (michaelz_at_iastate.edu)
Date: Tue Mar 22 2011 - 15:11:30 CDT

NAMD Users,

I want to do RBCG simulations on some large systems, but have been unable to
build RBCG models for small proteins (like 1UBQ) due to "*Error: failed on
end of **segment; molecule destroyed.*" errors. These are errors for
applying the NTER and CTER patches. If I try to set these to NONE then
autopsf also fails. Following the advice of:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/11194.html
and
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/14725.html

I have tried to source a different version of autopsf, but I don't see how
to do so. I have tried to at the tk console, but get: "*conflicting
versions provided for package "autopsf": 1.3, then 1.2*"

If anyone has further advice on making RBCG models, or a working RBCG model
that I could learn from, I would appreciate it.

Also, is there any news about using MARTINI in NAMD (
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/8802.html)?

I am using VMD v.1.9 Windows OpenGL, CUDA on 64-bit WinXP.

-- 
Michael Zimmermann
Ph.D. student in Bioinformatics and Computational Biology
Department of Biochemistry, Biophysics and Molecular Biology
Iowa State University

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