gnina/gnina issues and pull requests

#302 - Questions Regarding CrossDock2020 Dataset

Issue - State: open - Opened by wilson-lee1 23 days ago - 2 comments

#301 - ./gnina: error while loading shared libraries: libcudart.so.12: cannot open shared object file: No such file or directory

Issue - State: closed - Opened by JonasLi-19 28 days ago - 1 comment

#300 - When to ignore Open Babel warnings about ligands

Issue - State: closed - Opened by pjspol 29 days ago - 1 comment

#299 - Where is the comparison of three CNN models ? dense_1_3, dense_1_3_PT_KD_3, crossdock_default2018_KD_4

Issue - State: open - Opened by JonasLi-19 30 days ago - 1 comment

#298 - Issue with Incorrect Bond Orders in GNINA Output

Issue - State: open - Opened by satyabrata-uvm about 1 month ago - 1 comment

#297 - --cnn_outputdx and --cnn_outputxyz issue

Issue - State: open - Opened by Jalil-Mahdizadeh about 1 month ago

#296 - full_flex_output?

Issue - State: open - Opened by hajnal-adam about 1 month ago

#295 - Exporting data from "pose_sort_order"

Issue - State: closed - Opened by gcverissimo about 1 month ago - 2 comments

#294 - Discrepancy between Vina and CNN-based Scoring in gnina Docking: Which Metrics to Trust?

Issue - State: open - Opened by zhq90 about 1 month ago - 4 comments

#293 - Does GNINA support molecular docking of nucleic acid types?

Issue - State: open - Opened by LYZ02 about 1 month ago - 2 comments

#292 - Unable to install

Issue - State: open - Opened by snehachem 2 months ago - 6 comments

#291 - Another installation error

Issue - State: open - Opened by whitelord1994 2 months ago - 1 comment

#290 - Gnina 1.3 covalent docking doesn't return any output or error

Issue - State: closed - Opened by nitzan-simchi 3 months ago - 1 comment

#289 - Error when covalent docking: Provided ligand file format not supported with covalent docking.

Issue - State: closed - Opened by lovenicole 3 months ago - 3 comments

#288 - Gnina 1.3 Compilation on CentOS 7.9 with CUDA 12.1

Issue - State: open - Opened by amahany 3 months ago - 3 comments

#287 - Errors during installation procedure

Issue - State: closed - Opened by whitelord1994 3 months ago - 6 comments

#286 - Error in cmake

Issue - State: closed - Opened by xavgit 3 months ago - 3 comments

#285 - Non-GPU setup error

Issue - State: closed - Opened by what-is-what 3 months ago - 3 comments

#284 - About vina scoring

Issue - State: open - Opened by khan-0920 4 months ago - 6 comments

#283 - No GPU detected, while GPU is available

Issue - State: closed - Opened by hajnal-adam 4 months ago - 2 comments

#282 - [CMake] Allow to force external libraries and fix policy issue

Pull Request - State: closed - Opened by RMeli 5 months ago - 3 comments

#281 - Torch supports NVIDIA AMD and Intel GPUs

Issue - State: closed - Opened by paraunie 5 months ago - 11 comments

#280 - jsoncpp include

Pull Request - State: closed - Opened by RMeli 5 months ago - 3 comments

#279 - Runtime error (out of memory)

Issue - State: closed - Opened by nomoresomethingwentwrong 5 months ago - 1 comment

#278 - empirical scoring functions used in each step

Issue - State: open - Opened by Lili-Cao 5 months ago - 10 comments

#277 - The ligand seems too big and kekulize error

Issue - State: open - Opened by LiviaPham 5 months ago - 1 comment

#276 - Unusually low scores

Issue - State: open - Opened by virginestra 5 months ago - 1 comment

#275 - grid box size in gnina input

Issue - State: open - Opened by croshong 5 months ago - 1 comment

#274 - flexible docking issue

Issue - State: open - Opened by DingLuoXMU 6 months ago - 8 comments

#273 - The cross-docking test set

Issue - State: closed - Opened by DingLuoXMU 6 months ago - 1 comment

#272 - Problem with libmolgrig at the make step.

Issue - State: open - Opened by xavgit 6 months ago - 2 comments

#271 - Covalent Docking SO2F to LYS

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

#270 - how to keep Hs after docking

Issue - State: open - Opened by Lili-Cao 7 months ago - 6 comments

#269 - make error during libmolgrid step

Issue - State: closed - Opened by claggner 8 months ago - 4 comments

#268 - Question regarding cnn_scoring and scoring

Issue - State: open - Opened by NikiKou 8 months ago - 5 comments

#267 - --cnn_center_x/y/z arguments

Issue - State: closed - Opened by fatih4534 8 months ago - 3 comments

#266 - rmsd values in gnina output

Issue - State: closed - Opened by Lili-Cao 8 months ago - 4 comments

#265 - Neural net scoring without docking

Issue - State: closed - Opened by AqemiArnold 8 months ago - 3 comments

#264 - Trouble install when in ubuntu without nvidia GPU

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

#263 - CMake error in v1.1

Issue - State: closed - Opened by NikiKou 9 months ago - 2 comments

#262 - water

Issue - State: open - Opened by Lili-Cao 9 months ago - 4 comments

#261 - Initial pose not within the box; ligand outside the box

Issue - State: open - Opened by ngran1 9 months ago - 1 comment

#260 - Keep all hydrogens on poses from GNINA

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

#259 - different scores meaning

Issue - State: open - Opened by Lili-Cao 9 months ago - 3 comments

#258 - Question regarding (new?) metropolis scoring schemes

Issue - State: open - Opened by Tonylac77 9 months ago - 1 comment

#257 - Failed for cmake to find proper version of CUDA installation when multiple CUDA are installed

Issue - State: closed - Opened by haotianteng 9 months ago - 3 comments

#256 - random seed

Issue - State: open - Opened by Lili-Cao 9 months ago - 9 comments

#255 - Installation Error: sudo make -j2 The Eigen/Array header does no longer exist in Eigen3. All that functionality has moved to Eigen/Core.

Issue - State: closed - Opened by mainguyenanhvu 10 months ago - 5 comments

#254 - When examining the interaction, the covalent bond is not displayed.

Issue - State: closed - Opened by kaishi-08 10 months ago - 7 comments

#253 - Beginner's question, how to judge the quality of results based on several scores?

Issue - State: open - Opened by stan1233 10 months ago - 3 comments

#252 - ify cuda path

Issue - State: closed - Opened by Rasekuro 10 months ago - 1 comment

#251 - Installation error: path is prefixed in the build directory.

Issue - State: open - Opened by rcrehuet 11 months ago - 4 comments

#250 - ginina install error

Issue - State: open - Opened by croshong 11 months ago - 3 comments

#249 - Compile error in gninalibobj

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

#248 - jsoncpp error

Issue - State: open - Opened by Evert-Homan 11 months ago - 7 comments

#247 - Gnina installation on WSL hosted Ubuntu 22.04

Issue - State: open - Opened by demos57 11 months ago - 3 comments

#246 - Aborted (core dumped)

Issue - State: open - Opened by debanjansen48 about 1 year ago - 3 comments

#245 - DeltaDeltaG

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

#244 - Inquiry Regarding flexible Protein-Ligand Conformation Ranking with Gnina

Issue - State: open - Opened by ldx022 about 1 year ago - 1 comment

#243 - could I choose cuda version in docker？

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

#242 - Covalent Docking Setup

Issue - State: open - Opened by debanjansen48 about 1 year ago - 4 comments

#241 - GNINA generating incorrect bond orders

Issue - State: open - Opened by Tonylac77 about 1 year ago - 3 comments

#240 - libmolgrid with custom typer

Issue - State: closed - Opened by jacobdurrant about 1 year ago - 1 comment

#239 - unable to install

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

#238 - Gnina installation on HPC

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

#237 - Check failed: end < layers_.size() (-1 vs. 0)

Issue - State: closed - Opened by PengfeiFang-sioc about 1 year ago

#236 - Error installing GNINA

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

#235 - Scores not output to output file when running containerized Gnina

Issue - State: open - Opened by JohnKirwan over 1 year ago - 5 comments

#234 - Is it possible to use purely CPU for CNN?

Issue - State: open - Opened by AquifersBSIM over 1 year ago - 7 comments

#233 - Not able to run gnina with receptor and ligand information

Issue - State: closed - Opened by dibya035643 over 1 year ago - 1 comment

#232 - Aborted Jobs and Core Dumping

Issue - State: open - Opened by scheah86 over 1 year ago - 3 comments

#231 - output sdf file doesn't have CNNscore/CNNaffinity

Issue - State: closed - Opened by JonasLi-19 over 1 year ago - 8 comments

#230 - GPU Failure on CNN

Issue - State: closed - Opened by scheah86 over 1 year ago - 5 comments

#229 - Core dumping issues

Issue - State: open - Opened by scheah86 over 1 year ago - 2 comments

#228 - Issues when using the '--cnn_scoring all' flag

Issue - State: open - Opened by svolk19-stanford over 1 year ago - 4 comments

#227 - cannot run 'apt-get update'

Issue - State: open - Opened by RJ-Li over 1 year ago

#226 - Python path setting question when install Gnina

Issue - State: closed - Opened by JonasLi-19 over 1 year ago - 1 comment

#225 - dockerfile for ubuntu outdated

Issue - State: closed - Opened by Dadiao-shuai over 1 year ago - 4 comments

#224 - error: no matching function for call to ‘libmolgrid::CallbackIndexTyper::CallbackIndexTyper AND error: no matching function for call to ‘libmolgrid::CallbackVectorTyper::CallbackVectorTyper

Issue - State: closed - Opened by leticrisassis over 1 year ago - 2 comments

#223 - Wrongly used cmake -DCUDA_ARCH_NAME=All ..

Issue - State: closed - Opened by Kerro-junior over 1 year ago - 1 comment

#222 - I want to reproduce the default2018 model, but ...

Issue - State: open - Opened by Dadiao-shuai over 1 year ago - 2 comments

#221 - Stray '\341' (was \240 previously) in redock_2018_1.def breaks make

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

#220 - Issues when using Ubuntu22.04 docker image

Issue - State: closed - Opened by JonasLi-19 over 1 year ago

#219 - The molecular structure changes after gnina docking simulation.

Issue - State: open - Opened by Blue1993 over 1 year ago - 1 comment

#218 - feat: added citation file

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

#217 - Runtime Error boost::thread_resource_error

Issue - State: closed - Opened by Kerro-junior over 1 year ago - 12 comments

#216 - How can I run python scripts in Gnina Docker?

Issue - State: closed - Opened by Kerro-junior over 1 year ago - 1 comment

#215 - Issues with Eigen array header during make

Issue - State: closed - Opened by svolk19-stanford over 1 year ago - 6 comments

GitHub / gnina/gnina issues and pull requests