kalininalab/alphafold_non_docker

Issues

• How can I change the value of the argument "--models_to_relax"?

  #78 opened 3 months ago by frtntik
  0

• How to run AlphaFold non docker in NVidia 4090 card?

  #77 opened 5 months ago by longbow0
  0

• FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpzszd_m92/output.a3m'

  #76 opened 7 months ago by 33LIKL
  0

• Minimization failed after 100 attempts.

  #51 opened 2 years ago by dahaigui
  4

• Looking for more options for subsampling

  #74 opened 7 months ago by velocirraptor23
  2

• Too many command-line arguments.

  #64 opened a year ago by kbrunnerLXG
  2

• Error while running Alphafold without docker

  #32 opened 7 months ago by Comp-era
  3

• CUDA runtime implicit initialization on GPU:0 failed. Status: unrecognized error code

  #33 opened 7 months ago by Feng-Zhang
  1

• Error: Falling back to the CUDA driver for PTX compilation; ptxas does not support CC 8.9

  #75 opened 7 months ago by shadowdeng1994
  0

• Could not find HHBlits database

  #48 opened a year ago by karlaarz
  5

• ValueError: Could not find HHsearch database

  #72 opened 9 months ago by Lili-irtyd
  2

• Stuck on install step: https://github.com/deepmind/alphafold/archive does not exist

  #73 opened 8 months ago by bwllc
  1

• HHblits query running time is too long!

  #71 opened 10 months ago by JLHU2021
  0

• Why did I enter Python directly when running this Bash script?

  #70 opened a year ago by khanhtomiu
  0

• GPU Utilization verification

  #63 opened a year ago by rocketman8080
  1

• Unable to initialize backend 'tpu_driver'

  #68 opened a year ago by rocketman8080
  1

• zipfile.BadZipFile: File is not a zip file

  #67 opened a year ago by SHMinger
  0

• jaxlib==0.1.69+cuda111 still here and generating errors

  #52 opened 2 years ago by ocstx
  2

• 403 errors when trying to install Jax

  #66 opened a year ago by DanYousefi
  0

• Sequence length problem

  #65 opened a year ago by forever-happy-h
  0

• -p <use_precomputed_msas> flag not working

  #62 opened 2 years ago by gerdos
  1

• Update to Alphafold 2.3.0?

  #54 opened 2 years ago by avilella
  4

• Efficient use of multimer mode

  #59 opened 2 years ago by mpgriesh
  2

• Low GPU memory-usage and 0 GPU-Util

  #50 opened 2 years ago by xuxiaochen1209
  1

• Failed to allocate 50331648 bytes for new constant

  #55 opened 2 years ago by Violet969
  1

• Errors encountered when trying to run multimer mode

  #35 opened 3 years ago by mingyue80
  1

• Absolute path of download script

  #58 opened 2 years ago by zimb3l-priv
  3

• Error with Amber minimization toggle while running in multimer mode

  #43 opened 2 years ago by jcs0902
  1

• alphafold.data.tools

  #42 opened 2 years ago by as7a5
  1

• Taking a long time for predictions + more output files than expected

  #41 opened 2 years ago by kaymccoy
  3

• Taking very long time for protein structure prediction

  #40 opened 2 years ago by adi1bioinfo
  1

• RuntimeError: HHSearch failed:

  #37 opened 2 years ago by CristianoOliveira1
  2

• Couldn't get ptxas version string

  #26 opened 2 years ago by ihbxiongjie
  8

• "The preceding stack trace is the source of the JAX operation" error

  #23 opened 2 years ago by avilella
  7

• cuSolver error

  #22 opened 2 years ago by AnjaliSetiya
  1

• AttributeError: module 'jax.errors' has no attribute 'UnexpectedTracerError'

  #57 opened 2 years ago by ponomarevsy
  10

• Running AlphaFold-Multimer error

  #53 opened 2 years ago by mizzlefeng
  0

• Change of jaxlib-cuda wheel source

  #46 opened 2 years ago by quailwwk
  2

• ValueError: Could not find HHsearch database ./alphafold_data/pdb70/pdb70

  #47 opened 2 years ago by pariskang
  4

• Jax Version and pocketfft

  #45 opened 2 years ago by BlankSama
  5

• run only 1 of the 5 models for AF v2.2.0 monomer via bash command-line?

  #44 opened 2 years ago by avilella
  3

• Change in Alphafold 2.2.0 parameters

  #39 opened 3 years ago by abiadak
  1

• FATAL Flags parsing error

  #34 opened 3 years ago by mingyue80
  7

• Jax

  #29 opened 3 years ago by kdpan
  5

• jax update

  #31 opened 3 years ago by nick-youngblut
  1

• why pip instead of conda?

  #30 opened 3 years ago by nick-youngblut
  3

• Permission denied

  #28 opened 3 years ago by kdpan
  3

• Wrong variable names in download_database.sh

  #27 opened 3 years ago by Moa53
  1

• missing CIFS in pdb_mmcif?

  #25 opened 3 years ago by ryao-mdanderson
  2

• Incorrect variable name

  #24 opened 3 years ago by zappuf
  1