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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| Alexandre Bonvin PhD | Phone: (203) 432-5066 |
| Mol. Biophys. & Biochemistry | Fax: (203) 432-6946 |
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