AMBER Archive (2007)

Subject: AMBER: How to decide extra-helical or intra-helical bulge conformation by PTRAJ ?

From: sychen (u8613020_at_msg.ndhu.edu.tw)
Date: Sun Nov 04 2007 - 06:46:09 CST

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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