AMBER parameters

From: Andreas Svrcek-Seiler <>
Date: Tue 1 May 2001 15:58:13 +0200 (CEST)

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.
So, has anyone else had 'problems' with the respective parameters ?

Thanks in advance for any hints
best regards
W. A. Svrcek-Seiler

           ( O O )
              o        Wolfgang Andreas Svrcek-Seiler
              o        (godzilla)
      .oooO            Tel.:01-4277-52733
      (   )   Oooo.
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Received on Tue May 01 2001 - 06:58:13 PDT
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