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GitHub / Valdes-Tresanco-MS/gmx_MMPBSA issues and pull requests
#314 - binding free energy calculation between covalently bonded ligand and protein
Issue -
State: closed - Opened by leiqian-nmsu almost 2 years ago
- 1 comment
#313 - [Question]: ValueError: could not convert string to float: '*************'
Issue -
State: closed - Opened by purvacart almost 2 years ago
- 2 comments
Labels: duplicate
#312 - [Doc]: Add a description of FINAL_DECOMP_MMPBSA.dat file to docs
Issue -
State: closed - Opened by marioernestovaldes almost 2 years ago
- 1 comment
#311 - [Question]: gmx_MMPBSA decomposition question
Issue -
State: closed - Opened by BigMary2001 almost 2 years ago
- 6 comments
#308 - [Doc]: ValueError: could not convert string to float: '*************'
Issue -
State: closed - Opened by sathishdasari almost 2 years ago
- 2 comments
#307 - How can use multiple CPU for gmx calculation?
Issue -
State: closed - Opened by phuochuynh99 almost 2 years ago
- 2 comments
#306 - [Question]: gmx_MMPBSA failed while parsing results to output files
Issue -
State: closed - Opened by asharp07 almost 2 years ago
- 5 comments
#305 - [Question]: positive ΔTotal using gmx_MMPBSA
Issue -
State: closed - Opened by BigMary2001 almost 2 years ago
- 3 comments
#304 - [Question]: Why is my △TOTAL positive?
Issue -
State: closed - Opened by Clare-xiong almost 2 years ago
- 12 comments
Labels: Inconsistent input files
#303 - [Bug-gmx_MMPBSA]: Calculating forces using `frcopt` for nonlinear PB equation.
Issue -
State: closed - Opened by akshay-chenna almost 2 years ago
- 9 comments
Labels: wontfix
#302 - [leaprc for CHARMM force-field]:
Issue -
State: closed - Opened by sathishdasari almost 2 years ago
- 2 comments
Labels: charmm, topology
#301 - [Bug-gmx_MMPBSA]: 3D-RISM model from the examples are not working
Issue -
State: closed - Opened by spalgit almost 2 years ago
- 11 comments
Labels: ParmEd
#300 - [Question]: MMPBSA_Error Could not find necessary program [cpptraj].
Issue -
State: closed - Opened by purvacart almost 2 years ago
- 3 comments
#299 - [Bug-gmx_MMPBSA]: No such file or directory: '../setup/_temp_top.top’
Issue -
State: closed - Opened by Valdes-Tresanco-MS almost 2 years ago
Labels: bug
#298 - [Bug-gmx_MMPBSA]: Alanine scanning
Issue -
State: closed - Opened by aptamer1234 almost 2 years ago
- 12 comments
#297 - [Bug-gmx_MMPBSA_test]: Protein-Protein
Issue -
State: closed - Opened by aptamer1234 almost 2 years ago
- 2 comments
Labels: topology
#296 - [Question]: How to understand the FINAL_DECOMP_MMPBSA.dat file?
Issue -
State: closed - Opened by Clare-xiong almost 2 years ago
- 9 comments
#295 - [Question]: Calculation of binding energy in a system with multiple ligands
Issue -
State: closed - Opened by immortalfame almost 2 years ago
- 8 comments
#294 - [Question]: MMPBSA_Error when querying .mol2 files
Issue -
State: closed - Opened by 2SSSCN almost 2 years ago
- 8 comments
#293 - [Question]: gmx_MMPBSA failed while parsing results to output files
Issue -
State: closed - Opened by wangshuai-simulation almost 2 years ago
- 8 comments
#292 - [Bug-gmx_MMPBSA]: `print_res` in &decomp namelist not accept "all"
Issue -
State: closed - Opened by jsjyhzy almost 2 years ago
- 5 comments
Labels: bug
#291 - [Bug-gmx_MMPBSA]: DNA-Protein complex with CHRAMM forcefield
Issue -
State: closed - Opened by BatoolMM about 2 years ago
- 5 comments
#288 - [Doc]: Need example with small-molecule cofactor, ie. a GTPase containing GDP and Mg2+
Issue -
State: closed - Opened by sammun-insitro about 2 years ago
- 2 comments
#287 - AMBER Topology from GROMACS simulation with modified forcefiel
Issue -
State: closed - Opened by wulfbear about 2 years ago
- 10 comments
#286 - MMPBSA_Error Could not find necessary program [ GROMACS ][Question]:
Issue -
State: closed - Opened by avinashkarkada about 2 years ago
- 7 comments
#285 - [Question]: unknown error when installing gmx_MMPBSA
Issue -
State: closed - Opened by leiqian-nmsu about 2 years ago
- 4 comments
#282 - [ENH]: add 3D-RISM-AI
Issue -
State: closed - Opened by marioernestovaldes about 2 years ago
- 1 comment
Labels: enhancement, xbfree
#280 - [Bug-gmx_MMPBSA]: Bug in gmx_MMPBSA: Alanine scanning
Issue -
State: closed - Opened by leiqian-nmsu about 2 years ago
- 16 comments
Labels: bug, documentation, alascan, cas_intdiel
#279 - [Bug-gmx_MMPBSA]: KeyError:"ie"
Issue -
State: closed - Opened by WXYWD about 2 years ago
- 5 comments
Labels: bug, Can't reproduce
#277 - [Question]: No module name parmed
Issue -
State: closed - Opened by Brandt84 about 2 years ago
- 5 comments
Labels: installation
#276 - Progress bar
Pull Request -
State: closed - Opened by Valdes-Tresanco-MS about 2 years ago
#275 - [Bug-gmx_MMPBSA]: endless loop of "Calculating complex contribution..." regardless of endframe count.
Issue -
State: closed - Opened by bee-wulf about 2 years ago
- 6 comments
#274 - TypeError: unhashable type: 'list'
Issue -
State: closed - Opened by bee-wulf about 2 years ago
- 3 comments
Labels: bug
#273 - [Question]: Positive Binding Energy
Issue -
State: closed - Opened by laiyii about 2 years ago
- 23 comments
Labels: needs revision, theory
#262 - CalcError: /share/apps/conda_envs/gmxMMPBSA/bin/cpptraj failed with prmtop COM.prmtop!
Issue -
State: closed - Opened by hima111997 about 2 years ago
- 3 comments
Labels: bug
#260 - [Bug-gmx_MMPBSA]: Sander fails: bad atom type
Issue -
State: closed - Opened by Valdes-Tresanco-MS about 2 years ago
- 1 comment
Labels: third-party package
#256 - [Doc]: Undesired visual effects on per-residue PyMOL visualization
Issue -
State: closed - Opened by Valdes-Tresanco-MS over 2 years ago
- 1 comment
Labels: documentation
#245 - Add SASA-Based Model for Conformational Entropy Calculations
Issue -
State: closed - Opened by marioernestovaldes over 2 years ago
Labels: enhancement, xbfree
#241 - Important information about the docs...
Issue -
State: closed - Opened by marioernestovaldes over 2 years ago
Labels: documentation, high priority
#239 - GBNSR6 model implementation
Pull Request -
State: closed - Opened by Valdes-Tresanco-MS over 2 years ago
- 1 comment
#228 - [Bug-gmx_MMPBSA]: Error Parsing results to output files
Issue -
State: closed - Opened by wusiru2019 over 2 years ago
- 26 comments
Labels: bug
#225 - [Question]: Applying GB-MMSA on backmapped coarse grained structures
Issue -
State: closed - Opened by srdjan125 over 2 years ago
- 4 comments
Labels: topology
#224 - Insertion code error (invalid literal for int() with base 10: '52A')
Issue -
State: closed - Opened by drsandhyaks over 2 years ago
- 7 comments
Labels: duplicate, Inconsistent input files, ParmEd
#223 - [ENH]: Check compatibility with the new AmberTools22 code
Issue -
State: closed - Opened by marioernestovaldes over 2 years ago
- 2 comments
Labels: enhancement, third-party package
#220 - [Doc]: Improve tutorials
Issue -
State: open - Opened by marioernestovaldes over 2 years ago
Labels: documentation, improvement
#219 - [Question]: gmx_MMPBSA installation question
Issue -
State: closed - Opened by leiqian-nmsu over 2 years ago
- 15 comments
Labels: installation
#210 - [ENH]: Is it possible to use this tool for AMBER files?
Issue -
State: closed - Opened by aboelnga over 2 years ago
- 3 comments
Labels: enhancement, question, amber-files, xbfree
#200 - [ENH]: Add support for pbsa.cuda
Issue -
State: closed - Opened by marioernestovaldes over 2 years ago
- 5 comments
Labels: enhancement
#198 - [ENH]: Implement the PB calculation from APBS
Issue -
State: closed - Opened by Valdes-Tresanco-MS over 2 years ago
Labels: enhancement, xbfree
#196 - [ENH]: Add progress bar and estimated time to calculations
Issue -
State: closed - Opened by Valdes-Tresanco-MS over 2 years ago
- 2 comments
Labels: enhancement
#193 - Add Jupyter notebook support
Issue -
State: closed - Opened by marioernestovaldes over 2 years ago
Labels: enhancement, xbfree
#192 - Support for different MD programs
Issue -
State: closed - Opened by marioernestovaldes over 2 years ago
Labels: enhancement, xbfree
#178 - [ENH]: Remove topology generation from Structure
Issue -
State: closed - Opened by Valdes-Tresanco-MS over 2 years ago
Labels: improvement, xbfree
#177 - [ENH]: Support explicit water molecules
Issue -
State: closed - Opened by marioernestovaldes over 2 years ago
Labels: enhancement, xbfree
#174 - [ENH]: Add support for Delphi calculations
Issue -
State: closed - Opened by marioernestovaldes over 2 years ago
- 1 comment
Labels: enhancement, xbfree
#163 - mpi4py issue in gmx_MMPBSA installation
Issue -
State: closed - Opened by Atulsingh17 over 2 years ago
- 9 comments
Labels: python version
#161 - [ENH]: Add new radii sets...
Issue -
State: closed - Opened by marioernestovaldes over 2 years ago
- 3 comments
Labels: enhancement, xbfree
#157 - [ENH]: Allow index group name for group selection
Issue -
State: closed - Opened by wrmartin over 2 years ago
- 5 comments
Labels: enhancement
#153 - [Bug-gmx_MMPBSA]: change 3D-RISM calculation to sander
Issue -
State: closed - Opened by marioernestovaldes over 2 years ago
- 2 comments
Labels: needs revision
#123 - Docker container
Issue -
State: closed - Opened by Valdes-Tresanco-MS over 2 years ago
- 2 comments
Labels: enhancement, xbfree
#111 - Add GBNSR6 support
Issue -
State: closed - Opened by Valdes-Tresanco-MS over 2 years ago
- 3 comments
Labels: improvement
#87 - Add support for Plotly
Issue -
State: closed - Opened by Valdes-Tresanco-MS almost 3 years ago
- 1 comment
Labels: enhancement, xbfree
#84 - error while running gmx_MMPBSA
Issue -
State: closed - Opened by hima111997 almost 3 years ago
- 4 comments
Labels: wontfix, Inconsistent input files, unsupported force field
#57 - OverflowError on IE calculation
Issue -
State: closed - Opened by vsdepontes about 3 years ago
- 11 comments
#15 - trjconv failed when querying md.tpr
Issue -
State: closed - Opened by mar-ko2020 over 3 years ago
- 13 comments
Labels: Inconsistent input files