Dear Xplorers,
I'm trying to refine an RNA stem-loop and I have troubles with the
sugarconformations. The default parameters (which I obtained from
http://ndbserver.rutgers.edu/ndb/refinement/publish-geometry.html
(are those the most recent available?)) are meant for a 3'-endo conformation.
For the stem residues this works fine, but for residues in the loop and those
interacting with protein it doesn't. In the same parameter file defaults for
2'-endo are given. I tried feeding Xplor with both these sets of parameters
using the MULT statement.
In the manual it says that Xplor will handle multiple sets of parameters as
if it would involve different atom sets. Accordingly, the dihedral energy
increases (so far so good). I don't understand, however, how a dihedral can end
up in one of the energy minimums. If it does, it will always have a higher
energy for the second (and third and so on) set of parameters. In this way the
ideal value becomes one in between the two (in the case of RNA).
And this is actually what I observe. Sugars which showed a nice 3'-endo
conformation when I used only the 3'-endo defaults had adopted an unnatural
conformation with both the 3' and 2' endo, the former more than the latter. A
2'-exo sugar became 3'-endo (which is, in fact, the same difference). Is there
someone who hade the same problems? Any help will be appreciated.
Thanks,
Sjoerd
PS: I started with the same coordinates to compare the 'effect' of the
different parameter files.
