Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

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

#322 - How to add atom types to Vina?

Issue - State: open - Opened by Aochzh 19 days ago

#321 - Autodock Vina Scoring Functions

Issue - State: open - Opened by NeginManshour 20 days ago - 3 comments

#320 - Virtual screening using Python bindings

Issue - State: closed - Opened by eunos-1128 21 days ago - 7 comments

#319 - Method to capture receptor structure state after flexible docking

Issue - State: open - Opened by eunos-1128 24 days ago - 7 comments

#318 - FLexible Autodock

Issue - State: open - Opened by Kapalisuri 25 days ago - 1 comment

#317 - Charged ligands and receptors

Issue - State: closed - Opened by vsheg 26 days ago - 2 comments

#316 - Error on running prepare_flexreceptor.py for flexible docking

Issue - State: closed - Opened by eunos-1128 26 days ago - 8 comments

#315 - Problem in generation of some map files during flexible autodock docking.

Issue - State: open - Opened by aditya-jugade about 1 month ago - 3 comments

#314 - Issue : An internal error occurred in ../../../src/lib/tree.h(101)

Issue - State: open - Opened by Yannlefrancois about 1 month ago - 3 comments

#313 - Differences between `*_rigid.pdbqt` and `*.pdbqt` files of receptors

Issue - State: closed - Opened by eunos-1128 about 1 month ago - 2 comments

#312 - Flexible docking tutorial : no HD map file after autogrid4

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

#311 - H-bond term

Issue - State: open - Opened by h4RkhW8t53e about 2 months ago - 2 comments

#310 - I am getting this error while doing flexible autodock docking

Issue - State: open - Opened by aditya-jugade about 2 months ago - 1 comment

#309 - Vina runtime error: The ligand is outside the grid box

Issue - State: open - Opened by srilekha1993 about 2 months ago - 1 comment

#308 - Autogrid4 Unknown receptor type:

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

#307 - Problems with Binary installation

Issue - State: closed - Opened by HeheHahaHoHoHo about 2 months ago - 1 comment

#306 - rdkit.six not found

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

#304 - Vina flexible docking

Issue - State: open - Opened by aditya-jugade 2 months ago - 4 comments

#303 - Docking to zinc atoms in a non-3,1 tetrahedral conformation

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

#302 - Is AutoDock-Vina applicable to peptides?

Issue - State: open - Opened by SoodabehGhaffari 2 months ago - 3 comments

#301 - Weird protein split in flexible docking

Issue - State: open - Opened by farmaceut 3 months ago - 7 comments

#300 - Enormous free energy of binding

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

#299 - Autogrid4 raise error "dyld: Library not loaded:"

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

#298 - An internal error occurred in ../../../src/lib/parse_pdbqt.cpp(69).

Issue - State: open - Opened by jianwen350 3 months ago - 3 comments

#297 - Autogrid4 Atom Type Error with Large Ligand Database

Issue - State: open - Opened by R-Stefano 3 months ago - 6 comments

#296 - Details on scoring function terms

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

#295 - Python bindings vina v.s vina executable

Issue - State: closed - Opened by rytakahashi 3 months ago - 13 comments

#294 - Can't install 1.2.5 on Win11

Issue - State: closed - Opened by Evert-Homan 3 months ago - 2 comments

#293 - Large protein optimizations

Pull Request - State: open - Opened by jacktday 3 months ago

#292 - Flexible docking of Autodock using vina

Issue - State: open - Opened by Kapalisuri 3 months ago - 7 comments

#291 - Problems with Ruthenium

Issue - State: closed - Opened by sdevita7 3 months ago - 2 comments

#290 - Release v1.2.5

Issue - State: open - Opened by alchymy 3 months ago - 13 comments

#289 - How to use vina for small molecule and small molecule docking

Issue - State: open - Opened by yaqiuu 3 months ago - 1 comment

#288 - Can Autodock Vina perform Constraint Docking?

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

#287 - How can I add 2+ to metal atoms using `prepare_receptor`?

Issue - State: closed - Opened by eunos-1128 4 months ago - 9 comments

#286 - Charges in Vina

Issue - State: closed - Opened by Anujkumarp 4 months ago - 1 comment

#285 - Clarification on hydrophobic interaction contribution

Issue - State: closed - Opened by toby-aqemia 4 months ago - 2 comments

#282 - What is the difference between ADFR and flexible docking using vina?

Issue - State: closed - Opened by eunos-1128 4 months ago - 2 comments

#281 - Fix docstrings to include `vinardo` for python bindings

Pull Request - State: open - Opened by eunos-1128 4 months ago

#280 - keep key amino acid residues when docking

Issue - State: open - Opened by TVect 4 months ago - 2 comments

#279 - Tips for docking performance

Issue - State: closed - Opened by TVect 4 months ago - 1 comment

#278 - Remove duplicated calculation of coordinates.

Pull Request - State: open - Opened by shishaochen 5 months ago

#277 - Update README for using python APIs

Pull Request - State: closed - Opened by eunos-1128 5 months ago

#276 - Hydrated docking for ligands containing halogen atoms

Issue - State: closed - Opened by moabe84 5 months ago

#275 - Flexible hydrated docking

Issue - State: open - Opened by moabe84 5 months ago

#274 - Autodock vina error ------ "killed" while running

Issue - State: open - Opened by Soumyadutta03 5 months ago - 1 comment

#273 - Excessive time taking for vina to run

Issue - State: open - Opened by Soumyadutta03 5 months ago - 3 comments

#272 - converting pdbqt files to sdf when not prepared with Meeko

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

#271 - Ligand(s) was(ere) not initialized.

Issue - State: closed - Opened by YvetteJxy 5 months ago - 3 comments

#270 - error while running AutoDock Vina (batch ligand)

Issue - State: closed - Opened by serenafrancisco 5 months ago - 5 comments
Labels: enhancement

#269 - Error- Insufficient memory

Issue - State: closed - Opened by Soumyadutta03 5 months ago - 3 comments

#268 - Error while running Vina for multiple ligand docking

Issue - State: open - Opened by mbilaltayyab 5 months ago - 7 comments

#267 - Internal error running vina

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

#266 - Vina not producing complex structures after running

Issue - State: closed - Opened by AlexisGGk 6 months ago - 8 comments

#265 - Using autobox in a docking search

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

#264 - An internal error occurred in ../../../src/lib/tree.h(101)

Issue - State: closed - Opened by YvetteJxy 6 months ago - 4 comments

#263 - Valgrind reports leak in ScoringFunction

Issue - State: open - Opened by envidian 6 months ago

#262 - Fix leak in Vina::m_scoring_function reported by valgrind

Pull Request - State: open - Opened by envidian 6 months ago

#261 - Covalent Docking Broken

Issue - State: closed - Opened by gorrie06 6 months ago - 7 comments

#260 - an error with pip install vina

Issue - State: open - Opened by tomlongcool 7 months ago - 4 comments

#259 - problems in docking with zinc metalloproteins

Issue - State: open - Opened by Liuxxxxxxy 7 months ago - 2 comments

#257 - How to add H-bond directionality in Vina?

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

#256 - Running without receptor

Issue - State: open - Opened by ale94mleon 7 months ago - 1 comment

#255 - Request for support for python 3.10 and 3.11

Issue - State: open - Opened by shreyasvinaya 7 months ago - 3 comments
Labels: enhancement

#254 - Issue with using ad4 ff with python

Issue - State: open - Opened by kmorisa 7 months ago - 25 comments

#253 - Unused Variable vdw_rij

Issue - State: open - Opened by CoryKornowicz 8 months ago

#252 - grid configuration

Issue - State: open - Opened by leticrisassis 8 months ago - 4 comments

#251 - How to generate Vina forcefield grid space?

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

#249 - Vina force field

Issue - State: open - Opened by mirjr 8 months ago - 3 comments

#248 - Hydrated docking

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

#247 - Fail when installing vina from pypi.org

Issue - State: open - Opened by BuiQuocDung1991 9 months ago

#246 - Vina_map size

Issue - State: open - Opened by Dadiao-shuai 9 months ago - 7 comments

#245 - Issue Installing Vina

Issue - State: open - Opened by zlsess17 9 months ago - 1 comment

#244 - Make include guards unique

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

#243 - How to set vina score to dock complex with metals?

Issue - State: open - Opened by Dadiao-shuai 10 months ago - 5 comments

#242 - The ligand is outside the grid box.

Issue - State: open - Opened by Dadiao-shuai 10 months ago - 5 comments

#241 - ADFR Fail to generate PDBQT for a protein.pdb

Issue - State: open - Opened by Kerro-junior 10 months ago - 5 comments

#240 - Torsional entropies for the Vina scoring function

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

#239 - check for ARM64 boost libraries

Pull Request - State: open - Opened by jmcclare 10 months ago

#238 - How can I calculate RMSD in hydrated Vina?

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

#237 - Update github actions' versions

Pull Request - State: open - Opened by emiliofernandes 10 months ago

#236 - compatibility boost >= 1.83

Pull Request - State: closed - Opened by jalegido 10 months ago - 2 comments

#235 - Autodock 4 docking automation script

Issue - State: closed - Opened by apaydinemre 10 months ago - 4 comments
Labels: question

#234 - Some confusion about how releases are made

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

#233 - Batch mode with vinardo scoring function

Issue - State: closed - Opened by helen-power 10 months ago - 2 comments

#232 - different score results from different no_of_poses parameter setting

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

#231 - different score values between score() vs energies() after docking

Issue - State: closed - Opened by jaehongshin 11 months ago - 3 comments

#230 - Unable to install autodock

Issue - State: open - Opened by Lancespace 12 months ago - 5 comments

#229 - Procedure of treating Fe2+ Ion

Issue - State: closed - Opened by biotechjs 12 months ago - 4 comments
Labels: question

#228 - ModuleNotFoundError: No module named 'MolKit'

Issue - State: closed - Opened by JeongSooNa 12 months ago - 1 comment

#227 - Problems compiling in MacBook Pro M2 with split

Issue - State: open - Opened by mixcoha 12 months ago

#226 - Vina run error

Issue - State: open - Opened by huanggh0321 12 months ago

#225 - Vina Internal Error

Issue - State: open - Opened by Virzuo 12 months ago - 1 comment

#224 - How can ligand pdbqt input files to AutoDock 4 be batched?

Issue - State: open - Opened by YoavShamir5 about 1 year ago - 1 comment