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(base) stefan@stefan-Latitude-5521:~$ MetalDock/metaldock -i mc_input.ini
SPACING BETWEEN GRID POINTS IS STANDARD SET TO 0.375 Å
BOX SIZE MUST BE INTEGER GRID POINTS WHICH WAS NOT FOUND
BOX SIZE S…
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When running the docking with multiple outputs unidock outputs multiple result tables like this:
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+-----------…
zas97 updated
6 months ago
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I was trying to use the Perl interface to OpenBabel to do some RMSD calculations and found I couldn't since key functionality seemed to be missing. Specifically, the ability to manipulate SWIG C arra…
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### Issue summary
Hi, I am trying to use GNINA for docking of macrocycles. However no matter if I use autobot_lig command and after the ligand extracted from the protein, or I enter xyz coordinates e…
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The get_coordinates_pdb function in calculate_rmsd.py would benefit from the inclusion of 'HETATM' when reading in coordinates and atoms.
https://github.com/charnley/rmsd/blob/cd8af499fb63529a1b5b1…
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@bannanc, was that a result of the analysis script, or do you know why so many lines are repeated?
vtlim updated
7 years ago
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Hi,
I want to calculate the RMSD of one residue with previous frame as reference. My idea was to use the rmsd_perres() with ref='previous', but this doesn't work. Other option would to call the funct…
dafwb updated
4 years ago
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Hi,
I have used vina-gpu with some ligands.
In the config file I have used the lines:
num_modes = 5
log = vina-gpu2_docking_res_small_sample_size.log
The first lines of the log file are the f…
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### Expected behaviour
Analysis of a `Universe` with on-the-fly transformation scales good (reasonable).
### Actual behaviour
The scaling performance is really bad even with two cores.
### Cod…
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Having a function to calculate the RMSD between small molecules whose atoms are not necessarily listed in the same order seems like it would be potentially very useful, although it would need some gra…