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forlilab
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Meeko
Interfacing RDKit and AutoDock
GNU Lesser General Public License v2.1
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GPF file prepared by Meeko
#87
vsheg
opened
4 months ago
2
merge_these_atom_types ignored when passed as json config to mk_prepare_ligand.py
#86
diogomart
opened
4 months ago
0
Given `WARNING: Flexible residue outside box.` when centering off of reactive res
#85
althea-hansel
closed
3 months ago
1
mk_export fails though pdbqt file contains smiles
#84
TommyBiomodellingAU
closed
4 months ago
3
Json Encoders and Decoders in Molsetups and Chorizo Residues
#83
psharma-sr
closed
1 month ago
1
Reactive docking 'residue HIS not in residue_params' error
#82
apaydinemre
closed
5 months ago
6
Merge option to write vina-style grid box file
#81
althea-hansel
closed
5 months ago
0
Create PDBQT file instead of string
#80
daoquangtung2411
closed
6 months ago
2
Reactive Docking - *.maps.fld is not generated and does not exist
#79
guzh970630
opened
7 months ago
6
Merge multiprocessing
#78
althea-hansel
opened
7 months ago
1
mk_prepare_receptor
#77
TommyBiomodellingAU
opened
7 months ago
3
mk_prepare_ligand.py Issue
#76
heqing-chriscao
opened
8 months ago
6
citation
#75
tubiana
opened
8 months ago
2
Different charges than prepare_ligand4.py
#74
echen1214
closed
8 months ago
2
Restored bonds and clashed waters present after ligand preparation
#73
alissonws
opened
8 months ago
5
Question about ring breaking rules
#72
rwxayheee
closed
9 months ago
10
ATOM syntax incorrect: "CG0" is not a valid AutoDock type.
#71
Le-Phung-Hien
closed
8 months ago
4
'G' atom in pdbqt
#70
lh12565
opened
10 months ago
7
Create PDBQT receptor file from protonated PDB file.
#69
Le-Phung-Hien
closed
10 months ago
2
"ReadMOLFile-Error: bad atom count" error when open exported .sdf file in PyMOL
#68
Le-Phung-Hien
closed
10 months ago
3
Problem with macrocycle docking
#67
daoquangtung2411
opened
10 months ago
4
mk_export.py: Using --original_input for gnina pdbqt results
#66
Le-Phung-Hien
closed
10 months ago
7
mk_export.py not parsing PDBQT scores
#65
tlhr
closed
10 months ago
3
mk_prepare_ligand.py should return a non-0 exit code if it failed to create the output
#64
xrobin
opened
10 months ago
0
mk_prepare_ligand.py can change the total charge of the processed molecule.
#63
xavgit
closed
10 months ago
6
mk_export.py Runtime error
#62
eightmm
closed
10 months ago
9
Bug while using --verbose
#61
althea-hansel
closed
11 months ago
1
test/rdkitmol_from_docking_test.py fails with meeko==0.5.0
#60
natsukium
closed
11 months ago
4
update version strings from v0.4.0 to v0.5.0
#59
diogomart
closed
11 months ago
0
Warn about deprecation when old API (v0.4) is used in v0.5
#58
diogomart
closed
11 months ago
1
Cannot read ions with PDBQTMolecule
#57
xrobin
closed
11 months ago
7
Add option for passing new, SMARTS-specified atomtypes
#56
althea-hansel
closed
11 months ago
2
Check that partial charges are real numbers
#55
diogomart
closed
11 months ago
1
Expose option to append SMARTS and atom type to default list
#54
diogomart
closed
11 months ago
2
problem about convert .pdbqt to .sdf
#53
dinghezier
closed
11 months ago
6
enumerate rotamers of tertiary amides with different substituents
#52
diogomart
opened
12 months ago
0
compatibility with AutoDock
#51
YoavShamir5
closed
11 months ago
1
Missing name line in REMARK lines
#50
gkxiao
opened
1 year ago
1
Problem about prepared ligand hydrogen
#49
FeiLiuEM
closed
11 months ago
2
Reactive docking
#48
diogomart
closed
11 months ago
1
retaining unique atom names in the .pdbqt file
#47
alfredoq
opened
1 year ago
0
Changing default configs of the preparator
#46
alfredoq
closed
1 year ago
18
exec ./mk_export.py file.dlg -o result.sdf got error print("Option -o/--output_filename incompatible with multiple input files", file=sys.stderr)
#45
zhiyixu
closed
1 year ago
9
Meeko -m Unrecognized for Preparing Macrocycles
#44
selmifiqhi
closed
1 year ago
1
Wildcards for results export
#43
mattholc
closed
1 year ago
1
write_pdbqt_string error for large molecules (protein)
#42
QJ-Chen
closed
1 year ago
2
`nan` for charges on input molecule
#41
BJWiley233
closed
1 year ago
4
Molecule not OK, refusing to write PDBQT
#40
lmdu
closed
1 year ago
4
handle H isotopes for making RDKit mols from SMILES
#39
diogomart
closed
1 year ago
0
.sdf of only clusters leads
#38
eneas77
closed
1 year ago
3
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