> > donor mask :ADE.N1
> > *acceptor mask :THY.N3 :THY.H3*
> > hbond distance 7 series hbond
> > trajout traj.peptide nobox
p.s. that duplex is fairly big for simulation and contains a lot of
mismatches, G-G, C-C, A-A, T-T; I hope that is what you want... The G-G
and A-A overlaps may be severe enough to lead to stability problems in MD
unless minimized appropriately.
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Received on Sun Oct 08 2006 - 06:07:12 PDT
