rty10
commented
3 years ago 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.
Circular DNA currently works by taking reference frame of structure, copying the first frame to the end, and then in optimization ensure use of "--hold-last-bp". Circular DNA options should be in place to automatically generate this addition in the code and add stipulation to emDNA_DNAElectrostaticsParams / BpCollectionElectrostaticEnergy files to prevent possibility of two charges occupying the same space.