Hi! I am trying to run obenergy on the TERRA Quadruplex (PDB Code 3IBK) and I
am having trouble getting MMFF94 force field to calculate the energy. I am
not sure what is causing this problem (I have only basic knowledge in
computational chemistry) and I was wondering if any of you can help me out.
SETTING UP BOND CALCULATIONS...
USING EMPIRICAL RULE FOR BOND STRETCHING 1-2 (IDX)...
COULD NOT FIND PARAMETERS FOR BOND 58-522 (IDX)...
obenergy: could not setup force field.
GAFF seems to run into errors but outputs an answer:
COULD NOT FIND VDW PARAMETERS FOR ATOM K, USING HYDROGEN VDW PARAMETERS
Ghemical fails to find a bunch of torsion parameters but also spits out an
answer.
UFF corrects a bunch of coordination for angles (lots of them, which is
worrisome) and produces an answer.
I might be mistaken, but it seems like energies calculated from different
force fields can't be compared to each other because by themselves the
potential energies have no meaning. So I'm not sure if some force fields are
giving me wack answers or are producing correct results at all.
I would very much like to use MMFF94 because it has been previously used in
Quadruplex Modeling experiments. I was wondering if the error is caused by a
flaw in the MMFF94 algorithm, or if it is something unique about 3IBK, or if
there is a rotten structure in the PDB file.
Thanks, I appreciate it!
- Eric
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