Comments (4)
It looks like the Python AaronTools is failing to figure out where the ligand stops - it thinks the entire structure is the ligand. For organometallic cases, it would just stop when it finds a metal. I'll need to take a closer look at this to see where exactly it's going wrong.
I did find a bug in the mapLigand.py script that caused it to basically not use the -c/--center flag, and I've fixed that. The mapLigand.py script that is now on GitHub should work for organic systems as long as you use the -c or --center flag.
That being said, AaronTools should be able to figure out the ligand in this case without being told what the center is, and I will be looking into a fix for that.
You could also manually specify which atom is the center and which atoms are the ligand atoms in the comment line of the file. I used this:
L:7-11,17-22,28-29,37-42,48-53,55-56,61-66 C:67
to specify the ligand atoms (L:
) and the boron center (C:
). It's a little bit of a mess because the ligand atoms are not grouped together in the file. For completeness, the command I used with this comment was mapLigand.py ts1.xyz -l 28,29=AcAc -o new.xyz
I think the Perl version is a bit less sophisticated when it comes to figuring out the ligand. If I recall correctly, all atoms that come after the center are assumed to be ligand atoms, so you would need to reorder the atoms and specify the center with C:
in the comment.
from aarontools.py.
Thanks a lot! I have successfully mapped ligand in this purely organic system by command line operation
you provided of AaronTools.
However, this approach does not seem to be able to achieve both ligand replacement and substrate modification at the same time due to changes in atomic number, I do this by python API of AaronTools before. So, if possible, I would suggest adding parameters to specify the central atom and ligands of the system for the map_ligand
function in Geometry
object.
from aarontools.py.
For the time being, you can run detect_components
prior to map_ligand
example:
from AaronTools.geometry import Geometry
geom = Geometry("ts1.xyz")
# set the boron atom as the center
# alternatively, use "67"
geom.detect_components("B")
geom.map_ligand("AcAc", "28,29")
geom.substitute("CF3", "68")
geom.write(outfile="ts1-AcAc-CF3.xyz")
from aarontools.py.
Thanks Dr. Schaefer! It works well.
from aarontools.py.
Related Issues (19)
- parsing ORCA double hybrid with RI HOT 2
- all_geom HOT 4
- thermochem error for T = 0K HOT 3
- write orca SMD HOT 2
- int grids ORCA 5 HOT 2
- problem parsing HOT 2
- B2PLYP-D3 = B2PLYPD3 HOT 2
- basis/ecp HOT 1
- A bug in the AaronTools.geometry.Geometry.map_ligand() function HOT 3
- Small bug in SubmitProcess HOT 1
- Gaussian 16 log file doesn't parse correctly HOT 1
- Hashing and comparison HOT 6
- file calculated_bond_lengths.json missing after installation via pip HOT 1
- Loading Gaussian16 Scan HOT 3
- Radii for lanthanides/actinides HOT 2
- substitute using IUPAC/SMILES is buggy HOT 1
- Better consistency between ORCA and Gaussian inputs HOT 10
- Allow use of BSE python module HOT 1
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from aarontools.py.