AMBER Archive (2001)

Subject: Implicit solvent MD with small RNA's

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Wed Feb 14 2001 - 10:52:56 CST

Dear Experts,
After several 'experiments' with MD runs of small (tri up to penta) loop
RNA structures containing also a 4 basepair stem using the GB
approximation for solvation effects I am very pleased with the results
concerning the looped regions (because averaged structures are very close
to experimentally determined structures).
BUT: loop closing basepairs are very unstable. G-U pairs can open and
close several times at 300K within 4 ns production runs.
A 10 ns run at 335 K even showed a conversion from 'wrong' to
'close to "right"' in the loop regin but the closing bp opened and closed
several times
although the G-U was replaced by G-C for stability at the higher target
temperature. It's important to note that the bp's not only open slightly
but these bases do an excessive sampling of accessible conformations
before re-closing. The rest of the stack always behaved well - so did the
loop-bases.
So:Did I omit something, is this behavior a 'normal' consequence of
not using 'real' solvent molecules, thereby neglecting the
mechanic/kinematic effects of these ?
Or is it something completely different ?

Any kind of hint is much appreciated
Thanks in advance,
best regards
W. A. Svrcek-Seiler

P.S.: I forgot to mention that I did not include the SASA and its
derivatives. Intuitively, this should counteract
base pair fraying but I doubt it would suffice to
keep the closing base pairs together. 

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