AMBER Archive (2007)

Subject: AMBER: short 2'OH-OP contacts in RNA

From: Jose Gallego (jgallego_at_cipf.es)
Date: Fri Aug 10 2007 - 11:22:35 CDT

When simulating an RNA hairpin system for NMR refinement in vacuo with a
distance-dependent dielectric (eedmeth=5) and ff99 or ff94 in amber 8.0, I
am getting very close contacts between 2'OH groups and phosphate oxygens (as
short as 1.34 A).

These close contacts go away (or turn to more reasonable values-about 1.7 A)
when using ff99 and the generalized Born solvation model (igb=1). Can
anybody give me some information as to why these close contacts should be
appearing? Quick NMR refinements require vacuum conditions with an
appropriate dielectric function.

Thanks,

Dr. José Gallego
Centro de Investigación Príncipe Felipe
Avda. Autopista del Saler 16-3
46013 Valencia, Spain

Tel. +34-963-289680
FAX +34-963-289701
jgallego_at_cipf.es
www.cipf.es

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