pablo-arantes / making-it-rain

Cloud-based molecular simulations for everyone

pablo-arantes/making-it-rain Issues

Issues regarding scripts to run MD Simulation
Updated 8 days ago
Protein_ligand.ipynb
Updated a month ago
PDB database structure containing small molecules with certain pattern not working in protein_ligand notebook
Updated a month ago
Simulating a metallo-protein Apo form
Updated a month ago
can't install dependencies
Closed 2 months ago
RMSD
Updated 2 months ago
Hi, Pablo sir kindly help me with running metalloproteins - ligand complex. I don't find a way to run them. Please suggest me what should i do now?
Closed 2 months ago
Protein_ligand.ipynb
Updated 2 months ago4
Continuing trajectory analysis from previous MD simulation
Updated 2 months ago1
Protein+Membranes.ipynb | Parameters to generate the topology
Updated 2 months ago1
Martini+cg2all.ipynb | Parameters to generate the Martini topology
Updated 2 months ago1
Hydrogen added to ligand against intent?
Closed 3 months ago
Protein_ligand.ipynb PDBFixer problem
Closed 3 months ago2
Error in provide the necessary input files
Closed 3 months ago1
protein_ligand.ipynb
Closed 3 months ago3
Glycam.ipynb Error generating Amber Topology
Closed 3 months ago1
Error in Protein_ligand.ipynb antechamber commands
Closed 3 months ago3
Ligand parameterization panda code error
Closed 3 months ago2
checkpoint frequency is "savcrd_freq" ?
Closed 4 months ago1
Can't run protein-nanoparticle simulation.
Closed 4 months ago1
Having Issues with the AlphaFold2+MD notebook about "no module named colabfold"
Updated 4 months ago1
protein_ligand Colab - Violation occurred on line 240 in file Code/Numerics/Optimizer/BFGSOpt.h
Closed 4 months ago3
Provide the necessary input files (cannot work)
Closed 6 months ago3
ligand_gaff.pdb not being created
Closed 6 months ago3
Can not install dependencies in all notebooks.
Closed 6 months ago7
TypeError: Unit "kilojoule/mole" is not compatible with Unit "kilojoule/(nanometer*mole)".
Closed 7 months ago5
Prof. Dr. Salahalmulla
Closed 6 months ago1
Install dependencies fault (can't work)
Closed 6 months ago3
Prof. Dr. Salahalmula
Closed 7 months ago5
It doesn't show the RMSD graphic with the protein-ligand
Closed 7 months ago2
NAMD
Closed 7 months ago1
GROMACS with ligand
Closed 7 months ago1
Simulating a metallo-protein with 2 ligands
Updated 7 months ago7
OS error
Closed 8 months ago2
There is no option to run MMGBSA in this code repo. Please fix it
Closed 10 months ago7
ff.Minimize(maxIts=1000) does not work for the Protein_Ligand script
Closed 10 months ago2
Protein-Nucleic Acid Complex Simulation.
Closed a year ago2
Error in 'Parameters to generate the topology'
Closed a year ago1
cannot generate topology
Closed a year ago4
Equilibration output error
Closed a year ago6
Error on module prolif during protein-ligand md
Closed a year ago2
ValueError: operands could not be broadcast together with shapes (2500,3) (0,3) (2500,3)
Closed a year ago
Is it possible to run a binding energy decomposation(per residue) for a protein(peptide)-protein(receptor) system, using amber here on Colab?
Closed a year ago1
NameError: name 'vol' is not defined
Closed a year ago2
Error on "Parameters to generate the molecule topology on GAFF2 force field:"
Closed a year ago1
install dependencies can't work
Closed a year ago9
Is it possible to simulate one protein and two ligands simultaneously?
Closed a year ago4
protein_ligand topology builder (vol is not defined)
Closed a year ago1
Issue with histidine residues
Closed a year ago2
Incorrect conversion of some ligands
Closed a year ago1