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Incorporate Circular DNA about emdna HOT 1 OPEN

rty10 avatar rty10 commented on September 3, 2024
Incorporate Circular DNA

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rty10 avatar rty10 commented on September 3, 2024

Ran a test optimization of structure X with no errors without AND with new Electrostatics code:
$ emDNA-cli --x3DNA-bp-input=X.dat --DNA-seqdep-model=IdealDNA --hold-last-bp --energy-progress --output-name=X
$ emDNA-cli --x3DNA-bp-input=X.dat --DNA-seqdep-model=IdealDNA --dh-electrostatics --hold-last-bp --energy-progress --output-name=X

Took structure X, copied the first frame as a new last frame to produce a circular structure (common practice). Ran a test optimization with a circular form of DNA, where the first and last base pair are the same in space.
$ emDNA-cli --x3DNA-bp-input=X.dat --DNA-seqdep-model=IdealDNA --hold-last-bp --energy-progress --output-name=X
The following error was given:
'terminate called after throwing an instance of 'std::logic_error'
what(): basic_string::_M_construct null not valid
Aborted'

Same error for when you try --dh-electrostatics

Doing circular optimizations in the past where the first and last base pair frames were the same never produced this error.

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