Any experience about DNA dg-sa for structural deter. by XPLOR

Alexandre Bonvin abonvin at volta.csb.yale.edu
Fri Mar 24 14:49:00 EST 1995


In article <9503250616.AA17530 at iris.bc.ntu.edu.tw>  
chuang at IRIS.BC.NTU.EDU.TW writes:

> I am doing a computer modelling work to determine a DNA structure by  
dg-sa
> protocol using XPLOR package. Does any people has the experience on this  
?
> 
> My trouble is in the dg_sub_embed step. Could you share your *.inp files  
with me, or give me some suggestions how to choose the subset atoms in DNA
> case?

In my experience and from what I have seen around here, substructure  
embedding for DNA/RNA is very tricky. The only thing to work seems
a full structure embedding (and here goes cpu!).
You could also consider ab initio or random simulated annealing (it's 
in the X-PLOR manual). 

The next release of X-PLOR should have torsion-angle dynamics which seems  
to perform quite well for ab initio or random SA with DNA...

Alexandre

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