Dear experts,
A thorough conformational search for RNA tetraloop conformations
showed that it is possible to find conformations that have a lower
potential energy (by up to 6 kcal/mol) than anything in the (structural)
vicinity of any experimental reference structure (no matter whether
the reacton field contribution was calculated with GB or FDPB).
A common feature of the 'best' artificial conformers was a smaller
contribution of the MM (bond + angle + dihedral) terms.
A test run with parm99.dat instead of parm94.dat indeed showed
smaller differences, but did not reverse the rankinq of 'experimental' vs.
'artificial'.
So, has anyone else had 'problems' with the respective parameters ?
Thanks in advance for any hints
best regards
W. A. Svrcek-Seiler
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o Wolfgang Andreas Svrcek-Seiler
o (godzilla)
svrci_at_tbi.univie.ac.at
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Received on Tue May 01 2001 - 06:58:13 PDT
