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pablo-arantes
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making-it-rain
Cloud-based molecular simulations for everyone
MIT License
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Is it possible to simulate one protein and two ligands simultaneously?
#66
nyubachi
closed
1 year ago
4
Issue with histidine residues
#65
harrynov22
closed
1 year ago
2
Incorrect conversion of some ligands
#64
nyubachi
closed
1 year ago
1
GPU Acceleration
#63
Sundharesan10
closed
1 year ago
1
Ligand protein interaction can't run
#62
Fahryshitpost
closed
1 year ago
2
AlphaFold2+MD.ipynb CalledProcessError in Install Dependencies pip install -q "jax[cuda11_cudnn805]>=0.3.8,<0.4"
#61
PhoenixGF
closed
1 year ago
3
Concatenate and align the trajectory Error
#60
soul-stormer
closed
1 year ago
1
Interaction energy
#59
farescre
closed
1 year ago
2
An issue report in MM-PBSA method to calculate the binding free energy
#58
zhenwilliam
closed
1 year ago
2
Install dependencies: ModuleNotFoundError: No module named 'openmm'
#57
rayx1
closed
1 year ago
9
MM-PBSA method to calculate the binding free energy+Interaction Energy
#56
farescre
closed
1 year ago
3
Topology
#55
ggalueduran
closed
1 year ago
6
Interaction Energy
#54
KAO-KI
closed
1 year ago
3
Parameters to generate the topology:
#53
KAO-KI
closed
1 year ago
2
RuntimeError: Failed to setup action.
#52
cxb505
closed
1 year ago
0
torch update command added before torchani
#51
quantaosun
closed
1 year ago
0
Loading the necessary input files
#50
KAO-KI
closed
1 year ago
5
Equilibration MD simulation Error
#49
dimkorov
closed
1 year ago
3
Install dependencies
#48
KAO-KI
closed
1 year ago
3
Protein_Ligand, Ligand as smiles
#47
kva0987
closed
1 year ago
1
Protein_ligand.ipynb pybel issue
#46
kva0987
closed
1 year ago
5
new issues
#45
zjl894150094
closed
1 year ago
3
openmm circular import
#44
kva0987
closed
1 year ago
3
Multible GPUs
#43
mohamedfadlalla
closed
1 year ago
1
Exception ignored in: 'MDAnalysis.lib.formats.libdcd.DCDFile._read_header' OSError: Reading DCD header failed: premature EOF found in DCD file
#42
marionamujal
closed
1 year ago
2
UsageError Protein_ligand tool: WARNING:openff.toolkit.utils.toolkit_registry:Warning: Unable to load toolkit 'OpenEye Toolkit'. The Open Force Field Toolkit does not require the OpenEye Toolkits, and can use RDKit/AmberTools instead. However, if you have a valid license for the OpenEye Toolkits, consider installing them for faster performance and additional file format support: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html OpenEye offers free Toolkit licenses for academics: https://www.eyesopen.com/academic-licensing WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
#41
sbolivara16
closed
1 year ago
1
UsageError: Line magic function `%%capture` not found
#40
spmolnar
closed
1 year ago
1
NameError: name 'mbondi' is not defined
#39
KAO-KI
closed
1 year ago
2
Gromacs_inputs
#38
cwilliamszf
closed
1 year ago
2
Dynamic simultation using Martini forcefiekd
#37
Alain-chavanieu
closed
1 year ago
2
Can't install dependencies
#36
srs1402
closed
1 year ago
2
Can't Install dependencies
#35
MuthuBIN
closed
1 year ago
7
How to Deal Metallo-proteins with an Organic Molecule as a Ligand?
#34
Ash1000
closed
1 year ago
1
How to enter a specific Ligand_isomer to generate a topology file
#33
Ash1000
closed
1 year ago
2
Install dependencies - Protein_ligand.ipynb
#32
KAO-KI
closed
1 year ago
2
Parameters to generate the topology - Making it rain: Cloud-based molecular simulations for everyone
#31
KAO-KI
closed
1 year ago
4
error running AF2 prediction
#30
kkorotkov27
closed
1 year ago
1
AttributeError: module 'jaxlib.pocketfft' has no attribute 'pocketfft'
#29
pharmozyme-rperez
closed
1 year ago
1
Simulation accuracy of making it rain pipeline
#28
rijuaxt
closed
1 year ago
4
DCD file does not exist
#27
dag2225
closed
2 years ago
4
Making it rain on local host
#26
rijuaxt
closed
2 years ago
1
Query on use of forcefeilds.
#25
Arikite-netizen
closed
2 years ago
1
Possiblity to append/continue simuations;
#24
Arikite-netizen
closed
2 years ago
3
Molecular Simulation on Protein Ligand Complex in Gromacs
#23
atultiwari
closed
2 years ago
3
Unable to open output file
#22
avinashkarkada
closed
2 years ago
4
RuntimeError: can not find /content/drive/MyDrive/GROMACS_MIR/1aki_prod_1.dcd
#21
avinashkarkada
closed
2 years ago
2
ImportError: cannot import name '_openmm' from 'openmm'
#20
paserbamr
closed
2 years ago
2
SyntaxError: invalid syntax
#19
avinashkarkada
closed
2 years ago
7
Problems concatenating trajectory
#18
alessandronascimento
closed
2 years ago
3
name 'vol' is not defined
#17
masoudrezaei
closed
2 years ago
4
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