pablo-arantes making-it-rain issues

pablo-arantes / making-it-rain

Cloud-based molecular simulations for everyone

MIT License

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issues

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ValueError: The topology and CHAIN trajectory files don't have the same number of atoms!

#116 johnnytam100 opened 1 day ago
0
Hbond and SASA

#115 hashimkardaar opened 3 days ago
0
Issues regarding scripts to run MD Simulation

#114 nilanjana1996 opened 2 weeks ago
1
Protein_ligand.ipynb

#113 raphaelolipitz opened 1 month ago
0
PDB database structure containing small molecules with certain pattern not working in protein_ligand notebook

#112 quantaosun opened 1 month ago
0
Simulating a metallo-protein Apo form

#111 saraujo2023 opened 1 month ago
0
RMSD

#110 Salahalmulla opened 2 months ago
0
can't install dependencies

#109 noumanistic closed 2 months ago
0
Martini+cg2all.ipynb | Parameters to generate the Martini topology

#108 sflores14 opened 2 months ago
1
Protein+Membranes.ipynb | Parameters to generate the topology

#107 sflores14 opened 2 months ago
1
Continuing trajectory analysis from previous MD simulation

#106 tegarachsendo opened 2 months ago
1
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?

#105 noumanistic closed 2 months ago
0
Protein_ligand.ipynb PDBFixer problem

#104 zjun028 closed 3 months ago
2
Ligand parameterization panda code error

#103 yuuhi1341 closed 3 months ago
2
Hydrogen added to ligand against intent?

#102 nyubachi closed 3 months ago
0
Error in Protein_ligand.ipynb antechamber commands

#101 zjun028 closed 3 months ago
3
Having Issues with the AlphaFold2+MD notebook about "no module named colabfold"

#100 itzfredz opened 4 months ago
1
Can't run protein-nanoparticle simulation.

#99 noumanistic closed 4 months ago
1
Glycam.ipynb Error generating Amber Topology

#98 pramsland closed 3 months ago
1
protein_ligand.ipynb

#97 kadhirmn closed 3 months ago
3
checkpoint frequency is "savcrd_freq" ?

#96 nyubachi closed 4 months ago
1
Error in provide the necessary input files

#95 Salahalmulla closed 3 months ago
1
Protein_ligand.ipynb

#94 zjun028 opened 6 months ago
4
Can not install dependencies in all notebooks.

#93 noumanistic closed 6 months ago
7
Provide the necessary input files (cannot work)

#92 Salahalmulla closed 6 months ago
3
Prof. Dr. Salahalmulla

#91 Salahalmulla closed 6 months ago
1
Install dependencies fault (can't work)

#90 ysa123-2 closed 6 months ago
3
Prof. Dr. Salahalmula

#89 Salahalmulla closed 6 months ago
5
ligand_gaff.pdb not being created

#88 agarrubio closed 6 months ago
3
TypeError: Unit "kilojoule/mole" is not compatible with Unit "kilojoule/(nanometer*mole)".

#87 sflores14 closed 7 months ago
5
GROMACS with ligand

#86 Eliel83 closed 7 months ago
1
NAMD

#85 Eliel83 closed 7 months ago
1
protein_ligand Colab - Violation occurred on line 240 in file Code/Numerics/Optimizer/BFGSOpt.h

#84 dimkorov closed 4 months ago
3
It doesn't show the RMSD graphic with the protein-ligand

#83 Eliel83 closed 7 months ago
2
OS error

#82 ShrikirtiAnand closed 8 months ago
2
Simulating a metallo-protein with 2 ligands

#81 sadiogo opened 9 months ago
7
Add install rdkit

#80 mainguyenanhvu opened 10 months ago
2
There is no option to run MMGBSA in this code repo. Please fix it

#79 mainguyenanhvu closed 10 months ago
7
ff.Minimize(maxIts=1000) does not work for the Protein_Ligand script

#78 totocotonio1 closed 10 months ago
2
Protein-Nucleic Acid Complex Simulation.

#77 SsemuyigaMHC closed 10 months ago
2
Error in 'Parameters to generate the topology'

#76 jcatiggay closed 11 months ago
1
Equilibration output error

#75 jdernic closed 11 months ago
6
cannot generate topology

#74 syhpd closed 11 months ago
4
Error on module prolif during protein-ligand md

#73 anchy2111 closed 11 months ago
2
ValueError: operands could not be broadcast together with shapes (2500,3) (0,3) (2500,3)

#72 buridan2 closed 1 year ago
0
NameError: name 'vol' is not defined

#71 jsnwx0 closed 1 year ago
2
Error on "Parameters to generate the molecule topology on GAFF2 force field:"

#70 chemuser168 closed 1 year ago
1
Is it possible to run a binding energy decomposation(per residue) for a protein(peptide)-protein(receptor) system, using amber here on Colab?

#69 Infinite-Rainfall closed 1 year ago
1
install dependencies can't work

#68 puguh173224 closed 1 year ago
9
protein_ligand topology builder (vol is not defined)

#67 imeldp96 closed 1 year ago
1