Ecosyste.ms: Issues

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GitHub / ccsb-scripps/AutoDock-GPU issues and pull requests

#253 - How to Disable Desolvation Parameters in AutoDock Scoring Function during Docking?

Issue - State: open - Opened by samdani1593 5 months ago - 3 comments
Labels: enhancement

#252 - Speeding up sum reductions in ADADELTA by using Tensor Cores

Pull Request - State: open - Opened by L30nardoSV 6 months ago - 5 comments

#251 - atom types: HS, NS, OS

Issue - State: open - Opened by chaninpark0806 6 months ago - 1 comment

#250 - Automatically dock entire directory contents

Pull Request - State: closed - Opened by atillack 6 months ago - 4 comments

#249 - about the error

Issue - State: open - Opened by c00jsw00 7 months ago - 1 comment

#248 - Added output for grid map reading errors.

Pull Request - State: closed - Opened by atillack 8 months ago - 1 comment

#247 - compilation on MacOS Sonoma with Intel CPU and GPU

Issue - State: closed - Opened by lassancejm 8 months ago - 2 comments

#246 - How to get the docking result with various conformation.

Issue - State: closed - Opened by SejeongPark8354 8 months ago - 2 comments

#245 - write-gpf.py file

Issue - State: closed - Opened by mirjr 8 months ago - 1 comment

#244 - Output file for docking.

Issue - State: open - Opened by vaghasiyautsav 9 months ago - 1 comment

#243 - AutoDock-GPU Virtual Screening

Issue - State: closed - Opened by apaydinemre 9 months ago - 4 comments

#242 - Is it good practice to remove bound proteins too?

Issue - State: open - Opened by syedzayyan 10 months ago - 1 comment

#241 - Problems with AutoDock-GPU compiled on a cluster

Issue - State: open - Opened by xavgit 10 months ago - 2 comments

#240 - Suggestions about the use AutoDock-GPU with NVIDIA A100 GPUs

Issue - State: open - Opened by xavgit 10 months ago - 3 comments

#239 - Seems OpenCL is faster than CUDA

Issue - State: open - Opened by daylight0-0 10 months ago - 5 comments

#238 - Zero Affinities with GPU but not in Vina

Issue - State: closed - Opened by syedzayyan 11 months ago - 2 comments

#236 - Autodock is not opening in my laptop.

Issue - State: open - Opened by Caterine1234 12 months ago - 3 comments

#235 - Different Default Save Path for dlg Files when Using RTX4090

Issue - State: closed - Opened by NiBoyang 12 months ago - 4 comments

#234 - Problem about the preparation process before docking

Issue - State: open - Opened by FeiLiuEM about 1 year ago - 6 comments

#233 - Increased maximum number of runs to 8192

Pull Request - State: closed - Opened by atillack about 1 year ago - 2 comments

#232 - Maximum number of --nruns

Issue - State: open - Opened by Mishakolok about 1 year ago - 5 comments

#231 - autogrid4: FATAL ERROR: Sorry, I can't find or open AD4_parameters.dat

Issue - State: closed - Opened by amir-tagh about 1 year ago - 7 comments

#229 - Passing a batch file using -B and saving using -N

Issue - State: open - Opened by mikelee-dev about 1 year ago - 1 comment

#228 - Interpreting results after using --flexres

Issue - State: open - Opened by TheTrebuchet about 1 year ago - 3 comments

#227 - Unable to use batch Docking

Issue - State: open - Opened by Anupam-5 about 1 year ago - 1 comment

#226 - covalent docking free energy estimate

Issue - State: closed - Opened by agoliaei about 1 year ago - 3 comments

#225 - Relative path for dpf import and batch files

Pull Request - State: closed - Opened by atillack about 1 year ago - 4 comments

#224 - unable to execute batch file operation(--filelist)

Issue - State: open - Opened by 28YOGESH about 1 year ago - 4 comments

#223 - How do you save the lowest energy of a docking simulation?

Issue - State: open - Opened by mikelee-dev about 1 year ago - 2 comments

#222 - Ensure later specified (i.e. on command line) modified pair parameters have priority

Pull Request - State: closed - Opened by atillack over 1 year ago - 2 comments

#221 - Is there a way to compile Autodock-GPU on Windows?

Issue - State: open - Opened by kotenok2000 over 1 year ago - 3 comments

#220 - support turing and ampere for CUDA

Pull Request - State: open - Opened by forrestjgq over 1 year ago

#219 - Multiple ligands docking to one receptor

Issue - State: closed - Opened by pnakliang over 1 year ago - 3 comments

#218 - Standard output

Issue - State: closed - Opened by pnakliang over 1 year ago - 5 comments

#217 - Boron atom type

Issue - State: open - Opened by almeida85 over 1 year ago - 3 comments

#216 - Error compiling AUtodock-GPU on WSL2 and other issues

Issue - State: open - Opened by ayeshafatma over 1 year ago - 1 comment

#215 - Salt bridge distance-based analysis

Issue - State: open - Opened by eneas77 over 1 year ago - 1 comment

#214 - .sdf output of clustering representatives

Issue - State: open - Opened by eneas77 over 1 year ago

#213 - Running with --flexres give extremely high Energy

Issue - State: open - Opened by BJWiley233 over 1 year ago - 4 comments

#212 - Fixed pdbqt reading and switch sprintf's for snprintf's.

Pull Request - State: closed - Opened by atillack over 1 year ago - 1 comment

#211 - Cannot Compile from source nor Run binary on WSL2

Issue - State: closed - Opened by randymojica over 1 year ago - 8 comments

#210 - Fix for potential buffer overflow in results processing

Pull Request - State: closed - Opened by atillack over 1 year ago - 1 comment

#209 - Error: buffer overflow detected: terminated Aborted (core dumped)

Issue - State: open - Opened by songyingit over 1 year ago - 8 comments

#208 - Added pose output reduction options

Pull Request - State: closed - Opened by atillack over 1 year ago - 1 comment

#207 - Error Compiling Autodock

Issue - State: open - Opened by jssantiagojr almost 2 years ago - 3 comments

#206 - Assign different arguments to different targets in the batch mode

Issue - State: open - Opened by NiBoyang almost 2 years ago - 5 comments

#205 - Maximum number of atoms is 256

Issue - State: closed - Opened by cjl232 almost 2 years ago - 1 comment

#204 - Adding new atom type to parameter file

Issue - State: open - Opened by Chunchumaruu almost 2 years ago - 1 comment

#203 - Output interacition count for contact analysis even when no interaction was found

Pull Request - State: closed - Opened by atillack almost 2 years ago - 1 comment

#202 - "Could not identify ligand atom type Ni"

Issue - State: closed - Opened by pattabik83 almost 2 years ago - 2 comments

#201 - Batch Mode only uses ONE thread after using python's multiprocessing

Issue - State: closed - Opened by NiBoyang almost 2 years ago - 3 comments

#199 - Invocations to __syncthreads() and barrier() in calcMergeEneGra{.cu/.cl}

Issue - State: open - Opened by L30nardoSV about 2 years ago - 1 comment

#198 - Flexres output for --gbest and --npdb

Pull Request - State: closed - Opened by atillack about 2 years ago - 2 comments

#197 - Flexible Residue Positions when Ligand is Docked

Issue - State: closed - Opened by Professor333 about 2 years ago - 2 comments
Labels: enhancement

#196 - Is docking with two receptors at the same time feasible?

Issue - State: closed - Opened by Glinttsd about 2 years ago - 4 comments

#195 - Fix for xml2dlg erroneously claiming no ligand or flexres was specified.

Pull Request - State: closed - Opened by atillack about 2 years ago - 2 comments

#194 - -gbest option not extracting the lowest energy docked pose

Issue - State: closed - Opened by alfredoq about 2 years ago - 2 comments

#193 - cannot perform contact_analysis

Issue - State: closed - Opened by alfredoq about 2 years ago - 5 comments

#192 - cudaGetDeviceCount failed initialization error

Issue - State: open - Opened by jrcodina about 2 years ago - 1 comment

#191 - New to CentOS

Issue - State: closed - Opened by jrcodina about 2 years ago

#190 - Unknown atom type

Issue - State: closed - Opened by Teohoho about 2 years ago - 3 comments

#189 - Add grid center output in DLG file Grid parameters section.

Pull Request - State: closed - Opened by atillack about 2 years ago - 1 comment

#187 - How to use autodock-GPU for covalent docking in batch mode?

Issue - State: open - Opened by Yongrui-Wang about 2 years ago - 3 comments

#186 - Unable to execute

Issue - State: open - Opened by parazue about 2 years ago - 1 comment

#185 - How to choose different Docking Search Parameter Algorithms?

Issue - State: open - Opened by Leo-T-Zang over 2 years ago - 2 comments

#184 - Analytical rotation coefficient gradient correction

Pull Request - State: closed - Opened by atillack over 2 years ago - 2 comments

#183 - Add support for SYCL/Data Parallel C++ (DPCPP)

Pull Request - State: open - Opened by emascarenhas over 2 years ago

#182 - MPI parallelization across GPUs of a multi-GPU in AutoDock-GPU

Issue - State: open - Opened by vlkale over 2 years ago - 3 comments

#182 - MPI parallelization across GPUs of a multi-GPU in AutoDock-GPU

Issue - State: open - Opened by vlkale over 2 years ago - 3 comments

#181 - Error while running check.py file

Issue - State: closed - Opened by Datadriven1 over 2 years ago - 2 comments

#181 - Error while running check.py file

Issue - State: closed - Opened by Datadriven1 over 2 years ago - 2 comments

#180 - void SetKernelsGpuData(GpuData*) error

Issue - State: open - Opened by alfredoq over 2 years ago - 3 comments

#180 - void SetKernelsGpuData(GpuData*) error

Issue - State: open - Opened by alfredoq over 2 years ago - 3 comments

#179 - fix/Fixes contact analysis ligand xml closing tag

Pull Request - State: closed - Opened by sisco0 over 2 years ago - 1 comment

#179 - fix/Fixes contact analysis ligand xml closing tag

Pull Request - State: closed - Opened by sisco0 over 2 years ago - 1 comment

#178 - Energy score difference between dlg/xml output and stdout output

Issue - State: closed - Opened by shouti-fredchang over 2 years ago - 2 comments

#178 - Energy score difference between dlg/xml output and stdout output

Issue - State: closed - Opened by shouti-fredchang over 2 years ago - 2 comments

#177 - Astex Test files not found

Issue - State: closed - Opened by sisco0 over 2 years ago - 2 comments

#177 - Astex Test files not found

Issue - State: closed - Opened by sisco0 over 2 years ago - 2 comments

#176 - feat/Enable Github Actions CI CMake build

Pull Request - State: open - Opened by sisco0 over 2 years ago - 1 comment

#176 - feat/Enable Github Actions CI CMake build

Pull Request - State: open - Opened by sisco0 over 2 years ago - 2 comments

#175 - Mismatched tag for XML output file

Issue - State: closed - Opened by andreisfc over 2 years ago - 1 comment

#174 - feat/Added CMakeLists.txt file to the project

Pull Request - State: open - Opened by sisco0 over 2 years ago - 6 comments

#174 - feat/Added CMakeLists.txt file to the project

Pull Request - State: open - Opened by sisco0 over 2 years ago - 6 comments

#173 - Port the build system to a CMake one and integrate into Github Actions CI

Issue - State: open - Opened by sisco0 over 2 years ago - 2 comments

#173 - Port the build system to a CMake one and integrate into Github Actions CI

Issue - State: open - Opened by sisco0 over 2 years ago - 2 comments

#172 - invalid device symbol

Issue - State: open - Opened by Jianzhong2020 over 2 years ago - 10 comments

#171 - Covalent docking, flex res specification in filelist, and bugfix for more than one ligand

Pull Request - State: closed - Opened by atillack over 2 years ago - 3 comments

#170 - Regarding sampling algorithms in covalent docking

Issue - State: open - Opened by Hong-Rui over 2 years ago - 5 comments

#169 - Fixes for Apple

Pull Request - State: closed - Opened by atillack over 2 years ago - 2 comments

#169 - Fixes for Apple

Pull Request - State: closed - Opened by atillack over 2 years ago - 2 comments

#167 - add Boron parameters

Pull Request - State: closed - Opened by diogomart over 2 years ago - 1 comment

#167 - add Boron parameters

Pull Request - State: closed - Opened by diogomart over 2 years ago - 1 comment

#166 - automatic processing tools for map.fld file

Issue - State: open - Opened by HBioquant over 2 years ago - 1 comment

#166 - automatic processing tools for map.fld file

Issue - State: open - Opened by HBioquant over 2 years ago - 1 comment