michellab/BioSimSpace issues and pull requests

#100 - RDKit hangs while computing MCS for certain ligand pairs.

Issue - State: closed - Opened by lohedges about 5 years ago - 17 comments
Labels: bug

#99 - Mapping/merging errors

Issue - State: closed - Opened by dlukauskis about 5 years ago - 21 comments
Labels: bug

#98 - Reading crystal waters

Issue - State: closed - Opened by dlukauskis about 5 years ago - 2 comments
Labels: bug

#97 - FEP equilibration

Issue - State: closed - Opened by dlukauskis about 5 years ago - 43 comments
Labels: bug

#96 - Issues with reading files

Issue - State: closed - Opened by ppxasjsm about 5 years ago - 1 comment

#95 - Options for updating commandline options are not passed in parametrisation

Issue - State: closed - Opened by ppxasjsm about 5 years ago - 7 comments
Labels: bug

#94 - Somd-freenrg error

Issue - State: closed - Opened by dlukauskis about 5 years ago - 3 comments
Labels: bug

#93 - Parameterising molecules with chains

Issue - State: closed - Opened by lohedges about 5 years ago - 5 comments
Labels: bug, help wanted, question

#92 - Cluster run issue

Issue - State: closed - Opened by dlukauskis over 5 years ago - 21 comments
Labels: bug

#91 - Sample ethane to methanol script with explicit amber.

Issue - State: closed - Opened by ppxasjsm over 5 years ago - 2 comments
Labels: bug

#90 - Remote notebook usage

Issue - State: closed - Opened by oliverdutton over 5 years ago - 5 comments

#89 - Improving GROMACS performance

Issue - State: open - Opened by ppxasjsm over 5 years ago - 12 comments
Labels: enhancement, help wanted

#88 - Wrongly detected ring breaking

Issue - State: closed - Opened by maxjump over 5 years ago - 15 comments
Labels: bug

#87 - Argument update

Pull Request - State: closed - Opened by ppxasjsm over 5 years ago

#86 - Cannot access tutorials

Issue - State: closed - Opened by atbogetti over 5 years ago - 3 comments

#85 - RDKit Dependency

Issue - State: closed - Opened by msuruzhon over 5 years ago - 3 comments
Labels: help wanted, question

#84 - Feat notebook

Pull Request - State: closed - Opened by chryswoods over 5 years ago - 9 comments

#83 - Merging devel into master for the 2019.1.0 release

Pull Request - State: closed - Opened by lohedges over 5 years ago

#82 - Mapping error for almost symmetrical molecules

Issue - State: closed - Opened by maxjump over 5 years ago - 27 comments

#81 - Conda install

Issue - State: closed - Opened by ppxasjsm over 5 years ago - 6 comments

#80 - Atom Mapping Error: Merge has changed the molecular connectivity

Issue - State: closed - Opened by maxjump over 5 years ago - 24 comments

#79 - Inconsistent free energies between reverse mappings

Issue - State: closed - Opened by jmichel80 over 5 years ago - 5 comments

#78 - PDB trajectory support

Issue - State: closed - Opened by ppxasjsm over 5 years ago - 1 comment

#77 - Another comparison between BSS and FESetup pert files

Issue - State: closed - Opened by jmichel80 over 5 years ago - 1 comment

#76 - Unexpected mapping with BSS.Align.matchAtoms

Issue - State: closed - Opened by jmichel80 over 5 years ago - 10 comments

#75 - Chaining BSS nodes in python

Issue - State: closed - Opened by jmichel80 over 5 years ago - 5 comments
Labels: enhancement, question

#74 - Inconsistency between SOMD input files produced by BSS and by FESetup

Issue - State: closed - Opened by jmichel80 over 5 years ago - 52 comments
Labels: bug

#73 - Mappings for perturbations involving fused rings

Issue - State: closed - Opened by jmichel80 over 5 years ago - 3 comments
Labels: enhancement, question

#72 - binding_freenrg_gmx process does not get killed neatly or runs on gmx

Issue - State: closed - Opened by ppxasjsm over 5 years ago - 2 comments

#71 - MacOS Installation

Issue - State: closed - Opened by msuruzhon over 5 years ago - 20 comments

#70 - combine.py protein- ligand clash

Issue - State: closed - Opened by SofiaBariami over 5 years ago - 7 comments

#69 - system from nvt equilibration cannot be run with npt equilibration

Issue - State: closed - Opened by ppxasjsm over 5 years ago - 3 comments

#68 - Run time error with BSS.Process.Somd

Issue - State: closed - Opened by jmichel80 over 5 years ago - 12 comments

#67 - bug with uploading input files in notebook

Issue - State: closed - Opened by jmichel80 over 5 years ago - 1 comment

#66 - Better box size inference during solvation

Issue - State: closed - Opened by ppxasjsm over 5 years ago - 13 comments

#65 - Issue with going from pdb to minimisation

Issue - State: closed - Opened by ppxasjsm over 5 years ago - 10 comments

#64 - prematch option to BSS.Align.matchAtoms not working

Issue - State: closed - Opened by jmichel80 over 5 years ago - 12 comments
Labels: bug

#63 - a Bioconda package would be great

Issue - State: closed - Opened by bgruening over 5 years ago - 11 comments
Labels: question, whishlist

#62 - Question about intended use of node.validate()

Issue - State: closed - Opened by jmichel80 over 5 years ago - 5 comments
Labels: question

#61 - Heating with Gromacs does not behave as expected

Issue - State: closed - Opened by ppxasjsm over 5 years ago - 4 comments

#60 - Bonding parameters for water missing in parm7: this may be related to issue #52

Issue - State: closed - Opened by ppxasjsm over 5 years ago - 7 comments

#59 - Solvate issue with non periodic system

Issue - State: closed - Opened by jmichel80 over 5 years ago - 4 comments

#58 - minimisation with generic MD engine

Issue - State: closed - Opened by ppxasjsm over 5 years ago - 3 comments

#57 - BSS Gateway question

Issue - State: closed - Opened by ppxasjsm over 5 years ago - 10 comments
Labels: question

#56 - Setting custom config, does not update process info in print out?

Issue - State: closed - Opened by ppxasjsm over 5 years ago - 3 comments

#55 - BioSimSpace on OS X cannot CI/CD because of failing SOMD

Issue - State: closed - Opened by chryswoods over 5 years ago - 7 comments

#54 - Scope for supporting non-orthorhombic periodic boxes

Issue - State: closed - Opened by jmichel80 over 5 years ago - 6 comments
Labels: question

#53 - Virtual sites

Issue - State: open - Opened by jmichel80 over 5 years ago - 4 comments
Labels: question

#52 - Failed gromacs to amber conversion

Issue - State: closed - Opened by jmichel80 over 5 years ago - 14 comments

#51 - Process.run() or process.start()

Issue - State: closed - Opened by ppxasjsm over 5 years ago - 2 comments

#50 - Latest devel does not run setup demo

Issue - State: closed - Opened by ppxasjsm over 5 years ago - 3 comments

#49 - Cannot find an MD package that supports format: Gro87

Issue - State: closed - Opened by chryswoods over 5 years ago - 10 comments

#48 - BSS read/write molecules woes

Issue - State: closed - Opened by jmichel80 over 5 years ago - 5 comments

#47 - BSS inputs for SOMD cannot be loaded by Sire in some instances

Issue - State: closed - Opened by jmichel80 over 5 years ago

#46 - Adding space property to a system

Issue - State: closed - Opened by jmichel80 over 5 years ago - 4 comments

#45 - Unexpected AtomEditor exception in custom BSS script

Issue - State: closed - Opened by jmichel80 over 5 years ago - 2 comments

#44 - Add descriptions to supported file extensions

Issue - State: closed - Opened by ppxasjsm over 5 years ago - 4 comments
Labels: whishlist

#43 - Issue when perturbing molecule

Issue - State: closed - Opened by msuruzhon almost 6 years ago - 23 comments

#42 - Rigid water conversion

Issue - State: closed - Opened by lohedges almost 6 years ago - 1 comment

#41 - Add support for reading perturbed topologies and pert files

Issue - State: closed - Opened by msuruzhon almost 6 years ago - 2 comments
Labels: enhancement, whishlist

#40 - Ligand charge differs between BioSimSpace and FESetup

Issue - State: closed - Opened by lohedges almost 6 years ago - 7 comments

#39 - Align Module Issues

Issue - State: closed - Opened by msuruzhon almost 6 years ago - 8 comments

#38 - Forward and backward mapping not symmetric

Issue - State: closed - Opened by ppxasjsm almost 6 years ago - 2 comments

#37 - Package inconsistency warning

Issue - State: closed - Opened by ppxasjsm almost 6 years ago - 2 comments

#36 - MD error with FESetup output

Issue - State: closed - Opened by ppxasjsm almost 6 years ago - 9 comments

#35 - OpenMM CUDA device bug

Issue - State: closed - Opened by lohedges almost 6 years ago - 2 comments

#34 - Inconsistencies in name of GROMACS executable

Issue - State: closed - Opened by lohedges almost 6 years ago - 4 comments

#33 - Missing hydrogens

Issue - State: closed - Opened by lohedges almost 6 years ago - 1 comment

#32 - Crystal waters

Issue - State: closed - Opened by lohedges almost 6 years ago - 18 comments

#31 - Solvating a system containing a merged molecule

Issue - State: closed - Opened by lohedges almost 6 years ago - 2 comments

#30 - Poor MCS mapping behaviour

Issue - State: closed - Opened by lohedges almost 6 years ago - 8 comments

#29 - typo in install script

Issue - State: closed - Opened by bertadenes almost 6 years ago - 1 comment

#28 - SOMD

Issue - State: closed - Opened by lohedges almost 6 years ago - 8 comments
Labels: question

#27 - Parametrization fail for CathS ligands in seperate PDBs

Issue - State: closed - Opened by JenkeScheen about 6 years ago - 2 comments

#26 - recognising multiple molecules in pdb output from flare

Issue - State: closed - Opened by ppxasjsm about 6 years ago - 3 comments

#25 - behaviour of setup.py

Issue - State: closed - Opened by ppxasjsm about 6 years ago - 4 comments
Labels: enhancement

#24 - Check atom names in BSS generated pert files

Issue - State: closed - Opened by jmichel80 about 6 years ago - 3 comments

#23 - BSS install

Issue - State: closed - Opened by jmichel80 about 6 years ago - 2 comments

#22 - SaveMolecules to accept directories as input

Issue - State: closed - Opened by ppxasjsm about 6 years ago - 1 comment
Labels: enhancement

#21 - Core dump on ssh without X forwarding

Issue - State: closed - Opened by ppxasjsm about 6 years ago - 5 comments

#20 - Known parameterisation and solvation limitations

Issue - State: closed - Opened by lohedges about 6 years ago
Labels: enhancement

#19 - Gromacs

Issue - State: closed - Opened by lohedges over 6 years ago - 4 comments

#18 - BioSimSpace install script

Issue - State: closed - Opened by jmichel80 over 6 years ago - 3 comments

#17 - Python packaging

Issue - State: closed - Opened by lohedges over 6 years ago - 8 comments

#16 - Should we wrap Sire System?

Issue - State: closed - Opened by lohedges over 6 years ago - 2 comments
Labels: enhancement, question

#15 - Clearer equilibration protocol options.

Issue - State: closed - Opened by lohedges over 6 years ago - 1 comment
Labels: enhancement, question

#14 - namespace convention

Issue - State: closed - Opened by jmichel80 over 6 years ago - 6 comments
Labels: question

#13 - Potential dataset for best practices hydration free energy node

Issue - State: closed - Opened by jmichel80 over 6 years ago - 1 comment
Labels: question

#12 - Cannot view more than 3 molecules

Issue - State: closed - Opened by chryswoods over 6 years ago - 2 comments
Labels: bug

#11 - Float dialog box broken

Issue - State: closed - Opened by chryswoods over 6 years ago
Labels: bug

#10 - BioSimSpace tutorial - interactive MD - proposal for Protocol API changes

Issue - State: closed - Opened by jmichel80 over 6 years ago - 2 comments
Labels: enhancement

#9 - BioSimSpace tutorial - minimisation.ipynb notebook

Issue - State: closed - Opened by jmichel80 over 6 years ago - 1 comment
Labels: enhancement

#8 - BioSimSpace - clearer parsing error reports?

Issue - State: closed - Opened by jmichel80 over 6 years ago - 2 comments
Labels: enhancement

#7 - BioSimSpace won't import

Issue - State: closed - Opened by chryswoods over 6 years ago - 4 comments
Labels: bug

#6 - BioSimSpace and mdtraj are clashing...

Issue - State: closed - Opened by chryswoods over 6 years ago - 5 comments
Labels: bug

#5 - import BioSimSpace should not import matplotlib implicitly

Issue - State: closed - Opened by chryswoods over 6 years ago - 9 comments
Labels: bug

#4 - nglview

Issue - State: closed - Opened by ppxasjsm over 6 years ago - 14 comments

#3 - amber.py demo hangs with minimisation OSX

Issue - State: closed - Opened by ppxasjsm over 6 years ago - 1 comment

#2 - Problems with amber and gfortran

Issue - State: closed - Opened by ppxasjsm over 6 years ago - 1 comment
Labels: solved

#1 - demo amber.py is failing on devel for me

Issue - State: closed - Opened by ppxasjsm over 6 years ago - 1 comment

GitHub / michellab/BioSimSpace issues and pull requests