[AMBER] Regarding forcefields for Z-DNA

From: Yogeeshwar Ajjugal <bo14resch11004.iith.ac.in>
Date: Tue, 24 Jan 2017 15:23:24 +0530

Dear amber users,

I have performed GPU MD simulations using 2 force fields for Z-DNA protein
complex , namely 1) ff99SB and 2) combined force field of DNA
(leaprc.DNA.OL15) and protein (leaprc.protein.ff14SB) of AMBER16. I observe
that in ff99SB simulations the Z-DNA conformation remains unchanged
whereas, in leaprc.DNA.OL15 specified simulations the conformation of Z-DNA
is completely transformed to B-DNA conformation. Hence, which of these
results is reliable? What should be the appropriate force field to study
Z-DNA conformation? It would be really helpful if you could help me out
with this issue. Thank you very much.

*Thanks & Regards,*

*Yogeeshwar Ajjugal*

*Ph.D ScholarC/O Dr.Thenmalarchelvi Rathinavelan*

*Dept Of Biotechnology,Indian Institute of Technology Hyderabad,*
*Kandi, Medak-502285.*
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Received on Tue Jan 24 2017 - 02:00:03 PST
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