On Wed, Jul 17, 2013, Alexander Button wrote:
> The scripts which I have attempted to execute are the
> script program_5.nab which generates the lowest energy base triad for three
> given bases and the script program_6.nab which assembles the triads into
> the lowest energy dimer.
I'm afraid these particular programs need a more-or-less complete rewrite.
> I then decided to change the force field to the leaprc.99SB force field.
> The script then successfully ran giving me the outputs taDT.triad.min.pdb
> and taDT.energy.dat. I examined the pdb and found that it contained two
> residues in a Watson-Crick base pair arrangement and one residue (the third
> base ) perpendicular to the other two and on top of some of the atoms.
I can reproduce this. The "problem" is that the original programs implicitly
assumed that the nucleotides in the residue libraries were in particular
orientations. This is a bad assumption, since it does not survive updating
the libraries as year go on.
If I were to try to build triplexes at this point, I would use distance
geometry techniques, rather than a complex and fragile combination of
rigid-body transformations. I think such functionality has survived the
changing of the underlying libraries, but you should still be prepared for
some non-trivial amount of experimentation.
Thanks for pointing out the problems here; I'm sorry that I don't see any
simple fix. Maybe someone else on the list has ideas. You might want to
start from a "good" triplex (one you built, or found in the pdb) and try to
modify the bases, keeping the backbone (nearly) intact.
I'll update the manual for the next release.
...regards...dac
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Received on Fri Aug 09 2013 - 10:30:03 PDT
