Ecosyste.ms: Issues

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GitHub / Valdes-Tresanco-MS/gmx_MMPBSA issues and pull requests

#327 - [Bug-gmx_MMPBSA]: gmx make_ndx failed when querying index.ndx when using GMX2023

Issue - State: closed - Opened by RazzyChen about 2 years ago - 6 comments
Labels: Can't reproduce, third-party package

#326 - [Bug-gmx_MMPBSA]: bad atom type: MN

Issue - State: closed - Opened by Valdes-Tresanco-MS about 2 years ago - 1 comment

#324 - Unknown variable rgbmax in &gb

Issue - State: closed - Opened by wangshuai-simulation about 2 years ago - 2 comments
Labels: bug

#323 - [ENH]: Implement the science chart format

Issue - State: closed - Opened by Valdes-Tresanco-MS about 2 years ago
Labels: xbfree

#321 - [ENH]: Better describe the panels

Issue - State: open - Opened by Valdes-Tresanco-MS about 2 years ago
Labels: documentation

#320 - [ENH]: Decomposition with video

Issue - State: closed - Opened by marioernestovaldes about 2 years ago
Labels: xbfree

#318 - Create CODE_OF_CONDUCT.md

Pull Request - State: closed - Opened by Valdes-Tresanco-MS about 2 years ago

#317 - Bug-gmx_MMPBSA]: Alanine scanning

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

#316 - gmx_MMPBSA_test Errors

Issue - State: closed - Opened by wangshuai-simulation about 2 years ago - 7 comments

#315 - IndexError while parsing dihedraltypes

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

#314 - binding free energy calculation between covalently bonded ligand and protein

Issue - State: closed - Opened by leiqian-nmsu about 2 years ago - 1 comment

#313 - [Question]: ValueError: could not convert string to float: '*************'

Issue - State: closed - Opened by purvacart about 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 about 2 years ago - 1 comment

#311 - [Question]: gmx_MMPBSA decomposition question

Issue - State: closed - Opened by BigMary2001 about 2 years ago - 6 comments

#308 - [Doc]: ValueError: could not convert string to float: '*************'

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

#307 - How can use multiple CPU for gmx calculation?

Issue - State: closed - Opened by phuochuynh99 about 2 years ago - 2 comments

#306 - [Question]: gmx_MMPBSA failed while parsing results to output files

Issue - State: closed - Opened by asharp07 about 2 years ago - 5 comments

#305 - [Question]: positive ΔTotal using gmx_MMPBSA

Issue - State: closed - Opened by BigMary2001 about 2 years ago - 3 comments

#304 - [Question]: Why is my △TOTAL positive?

Issue - State: closed - Opened by Clare-xiong about 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 about 2 years ago - 9 comments
Labels: wontfix

#302 - [leaprc for CHARMM force-field]:

Issue - State: closed - Opened by sathishdasari about 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 about 2 years ago - 11 comments
Labels: ParmEd

#300 - [Question]: MMPBSA_Error Could not find necessary program [cpptraj].

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

#298 - [Bug-gmx_MMPBSA]: Alanine scanning

Issue - State: closed - Opened by aptamer1234 over 2 years ago - 12 comments

#297 - [Bug-gmx_MMPBSA_test]: Protein-Protein

Issue - State: closed - Opened by aptamer1234 over 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 over 2 years ago - 9 comments

#295 - [Question]: Calculation of binding energy in a system with multiple ligands

Issue - State: closed - Opened by immortalfame over 2 years ago - 8 comments

#294 - [Question]: MMPBSA_Error when querying .mol2 files

Issue - State: closed - Opened by 2SSSCN over 2 years ago - 8 comments

#293 - [Question]: gmx_MMPBSA failed while parsing results to output files

Issue - State: closed - Opened by wangshuai-simulation over 2 years ago - 8 comments

#292 - [Bug-gmx_MMPBSA]: `print_res` in &decomp namelist not accept "all"

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

#291 - [Bug-gmx_MMPBSA]: DNA-Protein complex with CHRAMM forcefield

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

#287 - AMBER Topology from GROMACS simulation with modified forcefiel

Issue - State: closed - Opened by wulfbear over 2 years ago - 10 comments

#286 - MMPBSA_Error Could not find necessary program [ GROMACS ][Question]:

Issue - State: closed - Opened by avinashkarkada over 2 years ago - 7 comments

#285 - [Question]: unknown error when installing gmx_MMPBSA

Issue - State: closed - Opened by leiqian-nmsu over 2 years ago - 4 comments

#282 - [ENH]: add 3D-RISM-AI

Issue - State: closed - Opened by marioernestovaldes over 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 over 2 years ago - 16 comments
Labels: bug, documentation, alascan, cas_intdiel

#279 - [Bug-gmx_MMPBSA]: KeyError:"ie"

Issue - State: closed - Opened by WXYWD over 2 years ago - 5 comments
Labels: bug, Can't reproduce

#277 - [Question]: No module name parmed

Issue - State: closed - Opened by Brandt84 over 2 years ago - 5 comments
Labels: installation

#276 - Progress bar

Pull Request - State: closed - Opened by Valdes-Tresanco-MS over 2 years ago

#274 - TypeError: unhashable type: 'list'

Issue - State: closed - Opened by bee-wulf over 2 years ago - 3 comments
Labels: bug

#273 - [Question]: Positive Binding Energy

Issue - State: closed - Opened by laiyii over 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 over 2 years ago - 3 comments
Labels: bug

#260 - [Bug-gmx_MMPBSA]: Sander fails: bad atom type

Issue - State: closed - Opened by Valdes-Tresanco-MS over 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 almost 3 years ago - 26 comments
Labels: bug

#225 - [Question]: Applying GB-MMSA on backmapped coarse grained structures

Issue - State: closed - Opened by srdjan125 almost 3 years ago - 4 comments
Labels: topology

#224 - Insertion code error (invalid literal for int() with base 10: '52A')

Issue - State: closed - Opened by drsandhyaks almost 3 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 almost 3 years ago - 2 comments
Labels: enhancement, third-party package

#220 - [Doc]: Improve tutorials

Issue - State: open - Opened by marioernestovaldes almost 3 years ago
Labels: documentation, improvement

#219 - [Question]: gmx_MMPBSA installation question

Issue - State: closed - Opened by leiqian-nmsu almost 3 years ago - 15 comments
Labels: installation

#210 - [ENH]: Is it possible to use this tool for AMBER files?

Issue - State: closed - Opened by aboelnga almost 3 years ago - 3 comments
Labels: enhancement, question, amber-files, xbfree

#200 - [ENH]: Add support for pbsa.cuda

Issue - State: closed - Opened by marioernestovaldes almost 3 years ago - 5 comments
Labels: enhancement

#198 - [ENH]: Implement the PB calculation from APBS

Issue - State: closed - Opened by Valdes-Tresanco-MS almost 3 years ago
Labels: enhancement, xbfree

#196 - [ENH]: Add progress bar and estimated time to calculations

Issue - State: closed - Opened by Valdes-Tresanco-MS almost 3 years ago - 2 comments
Labels: enhancement

#193 - Add Jupyter notebook support

Issue - State: closed - Opened by marioernestovaldes almost 3 years ago
Labels: enhancement, xbfree

#192 - Support for different MD programs

Issue - State: closed - Opened by marioernestovaldes almost 3 years ago
Labels: enhancement, xbfree

#178 - [ENH]: Remove topology generation from Structure

Issue - State: closed - Opened by Valdes-Tresanco-MS almost 3 years ago
Labels: improvement, xbfree

#177 - [ENH]: Support explicit water molecules

Issue - State: closed - Opened by marioernestovaldes almost 3 years ago
Labels: enhancement, xbfree

#174 - [ENH]: Add support for Delphi calculations

Issue - State: closed - Opened by marioernestovaldes almost 3 years ago - 1 comment
Labels: enhancement, xbfree

#163 - mpi4py issue in gmx_MMPBSA installation

Issue - State: closed - Opened by Atulsingh17 almost 3 years ago - 9 comments
Labels: python version

#161 - [ENH]: Add new radii sets...

Issue - State: closed - Opened by marioernestovaldes almost 3 years ago - 3 comments
Labels: enhancement, xbfree

#157 - [ENH]: Allow index group name for group selection

Issue - State: closed - Opened by wrmartin almost 3 years ago - 5 comments
Labels: enhancement

#153 - [Bug-gmx_MMPBSA]: change 3D-RISM calculation to sander

Issue - State: closed - Opened by marioernestovaldes almost 3 years ago - 2 comments
Labels: needs revision

#123 - Docker container

Issue - State: closed - Opened by Valdes-Tresanco-MS about 3 years ago - 2 comments
Labels: enhancement, xbfree

#111 - Add GBNSR6 support

Issue - State: closed - Opened by Valdes-Tresanco-MS about 3 years ago - 3 comments
Labels: improvement

#87 - Add support for Plotly

Issue - State: closed - Opened by Valdes-Tresanco-MS over 3 years ago - 1 comment
Labels: enhancement, xbfree

#84 - error while running gmx_MMPBSA

Issue - State: closed - Opened by hima111997 over 3 years ago - 4 comments
Labels: wontfix, Inconsistent input files, unsupported force field

#57 - OverflowError on IE calculation

Issue - State: closed - Opened by vsdepontes over 3 years ago - 11 comments

#15 - trjconv failed when querying md.tpr

Issue - State: closed - Opened by mar-ko2020 about 4 years ago - 13 comments
Labels: Inconsistent input files