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GHeinzelmann
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BAT.py
The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy calculations on protein-ligand systems, compatible with the AMBER and OpenMM simulation packages.
MIT License
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Confused about setting l1_x, l1_y, l1_z
#40
ErikZhang-9762
closed
3 days ago
5
Need some example input files for tevb or m*evbc
#39
ErikZhang-9762
closed
3 days ago
3
running BAT.py on already execute simulations
#38
amara86
opened
1 month ago
3
Calculating absolute binding free energy for membrane proteins
#37
amara86
closed
4 weeks ago
1
suggestion: remove CONECT lines from protonated ligand files
#36
camattelaer
closed
3 months ago
2
Necessary requirements for usage
#35
GattiMh
closed
4 months ago
4
Missing build_files/lig.pdb error when running OpenMM FE simulation with default config
#34
NiklasTR
closed
5 months ago
3
Calculating absolute binding free energy for membrane protein - ligand complex system
#33
MihyunSeo
closed
8 months ago
4
Free energy calculation step not finding files from equilibration step
#32
mixarcid
closed
10 months ago
1
UnboundLocalError: cannot access local variable 'ratio' where it is not associated with a value
#31
rez3vil
closed
1 year ago
11
Example Crashes
#30
tkram01
closed
1 year ago
6
Input files preparation
#29
quantaosun
closed
1 year ago
3
Suggestion: SLURM support?
#28
jaketanderson
closed
2 years ago
3
Possible unreferenced variable
#27
jaketanderson
closed
2 years ago
5
Openmm version
#26
spadavec
closed
2 years ago
1
Free energy calculation file not found.
#25
ParkvilleData
closed
2 years ago
7
File missing - Get last state from equilibrium simulations
#24
giangpth
closed
2 years ago
5
implementation of option align_method
#23
fengmudong
closed
2 years ago
1
Note: The following floating-point exceptions are signaling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
#22
hfhfgo
closed
2 years ago
1
New option retain_ligand_protonation that skips babel and retains ligand protonation state
#21
fengmudong
closed
2 years ago
2
Constraints.in file was missing
#20
a-abdoman
closed
3 years ago
3
Question on correct behaviour for the ligand only phase.
#19
josiahbones
closed
3 years ago
1
Remove hydrogens
#18
GHeinzelmann
closed
3 years ago
1
Charged
#17
GHeinzelmann
closed
3 years ago
0
Move BAT.py to Amber20 only
#16
GHeinzelmann
closed
3 years ago
1
Ligand parameterization question
#15
tantrev
closed
3 years ago
1
Python 3
#14
GHeinzelmann
closed
3 years ago
1
OpenBabel 3.0
#13
GHeinzelmann
closed
3 years ago
1
Max. 500 TI atoms
#12
GHeinzelmann
opened
3 years ago
2
ligand charge option
#11
GHeinzelmann
closed
3 years ago
1
Protein and ligand protonation
#10
GHeinzelmann
closed
5 months ago
2
charged ligands (amber18)
#9
GHeinzelmann
closed
3 years ago
1
Charged ligands
#8
GHeinzelmann
closed
3 years ago
1
Amber20
#7
GHeinzelmann
closed
3 years ago
0
kinase acetonitrile system
#6
DDGmichigan
closed
3 years ago
14
Create analysis_AMBER20.py
#5
baba-hashimoto
closed
3 years ago
2
Update for use with AMBER20
#4
GHeinzelmann
closed
3 years ago
1
Charge detection during solvation
#3
GHeinzelmann
closed
4 years ago
1
some errors
#2
baba-hashimoto
closed
4 years ago
4
License missing
#1
CMargreitter
closed
4 years ago
1