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I'm using SVN openbabel through git avogadro. If SO3 (with a double S=O bond for each of the oxygens) is optimized, none of the available forcefields result in a planar shape, though ghemical gets ve…
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On line 2848 of the file src/forcefields/forcefieldmmff94.cpp, the units for theta2 are degrees^2. This causes the parameter anglecalc.ka to be two orders of magnitude smaller than the typical force c…
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Hi,
There is a bug in the atom type determination of terminal oxygens attached to Sulfurs, e.g. in the sulphonamide group S(=O)(=O)N.
Line 2339 on src/forcefields/forcefieldmmff94.cpp :
if (nb…
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@jchodera - via `conda`, we're still getting 0.1.2 from Omnia rather than 0.1.4. Is there something we have to do to get the build to update? @limn1 is having issues with this when attempting to get i…
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We would like to be able to use ligands set up with SMIRFF (to be renamed SMIRNOFF) together with proteins set up with AMBER or other forcefields. I think it should be possible to do this using ParmEd…
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First reported on the list by Bjoern Gruening on 27 Jul.
The following code exhibits causes a segfault on Windows (inchi.sdf attached):
==============
from cinfony import pybel
mols = list(pyb…
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### Quantum chemistry
| Description | Reference implementation | Status | Issues |
| -- | -- | -- | -- |
| DFT | PySCF | Done - 0.7.3 | |
| MP2 | PySCF | Done - 0.7.3 | |
| MCSCF | PySCF | Don…
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The installer on the main site, used to install a fresh copy of openbabel on a virgin 10.6.2 machine appears to install a broken version of openbabel that appears to not be able to do anything. Addit…
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When looking up a GROMACS dihedral type, apparently GROMACS chooses the _first_ entry that it finds, not the most specific (fewest wildcards).
```
[ dihedraltypes ]
X CT OH X …
ctk3b updated
7 years ago
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Downloaded and installed prebuilt executable (Avogadro2.0.8.0-Darwin).
When I click on optimize geometry or any button in extensions I get an error like this.
An error occurred while retrieving the li…