Dear all,
I'd like to use PTRAJ to decide whether extra-helical or intra-helical bulge conformation (even the level)
for ADE16 & ADE17 of the RNA fragment r(5'-GCGUCACACC-3')/r(5'-CGCUGAAGUGG-3') in a 20ns MD simulation by SANDER.
(The extra-helical for ADE15 & ADE16 structure is like the PDBID: 1PBR)
Is there any formula (implemented by dealing with several backbone parameters from PTRAJ) or publication on this issue?
Thank you!
Best Regards,
sychen.
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Received on Wed Nov 07 2007 - 06:07:06 PST
