David van der Spoel

Kekulization failure with charged ring

7

- [ X] I believe this to be a bug with Open Babel - [ ] This is a feature request ## Environment Information Open Babel version: master Operating system...

Implemented code for atom-typing to support the Alexandria force field.

1

The Alexandria Chemistry Toolkit for building force fields will be released shortly. It relies on the OpenBabel software to support it for generating atom types. In this patch the forcefieldalexandria...

itp file is not self-sufficient.

2

It would be good to add a link in the documentation of where to download the exact martini ff file corresponding to the itp file provided here.

Difficult to get low gradients

4

I have implemented your LBFGS implementation in my chemistry code and try to use it to minimize the energy of molecules using a classical potential function. For some compounds it...

Divide by zero error in line search

2

At line 40 in the linesearch.cpp code there is a divide by zero occurring. ``` double find_quadratic_minimizer(double a, double ga, double b, double gb) { return b + ((b -...

Floating point division by zero when running SAPT with H+ as a compound

4

When using H+ as the compound in a SAPT calculation it crashes with a divide by zero error: ``` File "/var/spool/slurm/d/job333055/slurm_script", line 21, in myener = psi4.energy("sapt2+(ccd)dmp2") File "/home/spoel/miniconda3/lib/python3.8/site-packages/psi4/driver/driver.py", line...

Attached script generates obmol objects from strings containing an xyz file. If I switch the order of the coordinates, the atom type assignment changes, that is, the hydrogen bound to...