Dear AMBER users,
I've modelled single-stranded poly(rC) with explicit water and
counterions starting from its helical conformation. But after 2.1 ns
production simulation my poly(rC) seems to be gone quite far from its
initial helical conformation (first snapshot). Backbone RMSD is
around 3 A (see attachment)).
The simulation protocol, I've used, is similar to that from the DNA
tutorial:
minimization of solvent and of the all system
20 ps heating from 0 to 300 with weak positional restraints on polyrC
200ps equilibration md
2.1 ns production run
How do you think, may be there is a problem in my simulation protocol
or such simulations are quite normal for single-stranded oligonucleotides?
How can I estimate he helicity of the distorted polyrC?
I'm new to AMBER so any suggestions of more experienced users would be
helpful.
With many thanks in advance,
Kat
mailto:kateryna_mirosh.ire.kharkov.ua
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Received on Mon Apr 04 2005 - 15:53:01 PDT
