Ecosyste.ms: Issues
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GitHub / Valdes-Tresanco-MS/gmx_MMPBSA issues and pull requests
#537 - [Bug-gmx_MMPBSA]: sander failed with prmtop COM.prmtop!
Issue -
State: open - Opened by dxf320 6 days ago
#536 - [Question]: Which file was used to create index.ndx file for binding energay caluclation?
Issue -
State: closed - Opened by Tangbbmc 8 days ago
- 6 comments
#535 - [Bug-gmx_MMPBSA_ana]: Analysis with QH runs prevent GUI analysis
Issue -
State: open - Opened by bdratch 12 days ago
#534 - test
Issue -
State: closed - Opened by Samuel-gwb 23 days ago
#533 - [Bug-gmx_MMPBSA_ana]: Could not import PyQt5/PyQt6
Issue -
State: open - Opened by mglgc about 1 month ago
- 2 comments
#532 - Update env.yml
Pull Request -
State: closed - Opened by pritampanda15 about 1 month ago
#531 - [Doc]: Alanine Scann issue
Issue -
State: open - Opened by julruiz72 about 1 month ago
- 1 comment
#530 - [Bug-gmx_MMPBSA]: Failed building wheel for pandas
Issue -
State: closed - Opened by hubertrybka about 2 months ago
- 2 comments
#529 - [Bug-gmx_MMPBSA]: failed with prmtop COM.prmtop!
Issue -
State: open - Opened by Simon-dumplings about 2 months ago
#528 - [Bug-gmx_MMPBSA]:
Issue -
State: closed - Opened by JuuelHerza about 2 months ago
- 8 comments
#526 - [Bug-gmx_MMPBSA]: ImportError with mpi4py
Issue -
State: closed - Opened by jstump-1999 2 months ago
- 4 comments
#524 - [Bug-gmx_MMPBSA]: teLeap Error
Issue -
State: open - Opened by mkoiral 2 months ago
- 30 comments
#523 - [Question]: Error: The complex, receptor, and ligand trajectories must be the same length.
Issue -
State: open - Opened by alanrodriguez06 2 months ago
- 1 comment
Labels: bug
#522 - [Question]: GromacsError: Only 3-point vsite type 1 is supported
Issue -
State: open - Opened by huaiaee 2 months ago
- 7 comments
#521 - [Questunable to get the decomposition result
Issue -
State: closed - Opened by suruchi-25 2 months ago
- 6 comments
#520 - [Bug-gmx_MMPBSA]:
Issue -
State: closed - Opened by suruchi-25 2 months ago
- 2 comments
#519 - [Issue-gmx_MMPBSA]: IndexError: list index out of range
Issue -
State: closed - Opened by Ossmonde 3 months ago
- 1 comment
#518 - [Question]: unable to understand the results
Issue -
State: open - Opened by suruchi-25 3 months ago
- 8 comments
#517 - [Question]: I am not able to install gmxmmpbsa on ubuntu 2024.
Issue -
State: open - Opened by AKR845 3 months ago
- 13 comments
#516 - [Bug-gmx_MMPBSA_ana]:KeyError : "delta"
Issue -
State: open - Opened by Arikite-netizen 3 months ago
- 1 comment
#515 - Installing gmx_MMPBSA on HPC using AmberTools method
Issue -
State: closed - Opened by ocampbel 3 months ago
- 5 comments
#514 - [Bug-gmx_MMPBSA]:
Issue -
State: closed - Opened by suruchi-25 3 months ago
- 4 comments
#513 - [Bug-gmx_MMPBSA_ana]: can not open gmx_MMPBSA_ana
Issue -
State: open - Opened by jackhu5 4 months ago
- 1 comment
#512 - [Bug-gmx_MMPBSA]: PyQt6/QtGui.abi3.so: undefined symbol: _ZN5QFont11tagToStringEj, version Qt_6
Issue -
State: closed - Opened by suruchi-25 4 months ago
- 1 comment
#511 - [Bug-gmx_MMPBSA]: Could not import PyQt5/PyQt6. gmx_MMPBSA_ana will be disabled until PyQt5/PyQt6 is installed
Issue -
State: closed - Opened by suruchi-25 4 months ago
- 1 comment
#510 - [Bug-gmx_MMPBSA]: TypeError: string indices must be integers
Issue -
State: closed - Opened by suruchi-25 4 months ago
- 7 comments
#509 - [Bug-gmx_MMPBSA]: gmx_MMPBSA: error: unrecognized arguments
Issue -
State: closed - Opened by suruchi-25 4 months ago
- 1 comment
#508 - [Question]: Handling Protein-Ligand Complexes Embedded in Membranes with LPH Atoms
Issue -
State: closed - Opened by huaiaee 4 months ago
- 5 comments
#507 - [Question]: Energy differences between WT and mutation
Issue -
State: open - Opened by WoutVanEynde 4 months ago
- 3 comments
#506 - [Question]: The results of multiple calculations are exactly the same
Issue -
State: closed - Opened by chanchanchanchanchan 4 months ago
- 9 comments
#505 - [Question: Building Normal Complex Amber Topology Error
Issue -
State: open - Opened by lvckyv 4 months ago
- 2 comments
#504 - [Question]: TypeError in res2map When Running Protein-Ligand Binding Free Energy Calculations
Issue -
State: closed - Opened by huaiaee 4 months ago
- 7 comments
#503 - [Question]: Facing trouble with mmpbsa sander and PB calculation for protein-ligand complex
Issue -
State: open - Opened by Rajath701 4 months ago
- 13 comments
#502 - [Question]: How to calculate the binding free energy of lipids membrane and peptide
Issue -
State: closed - Opened by chanchanchanchanchan 4 months ago
- 2 comments
#501 - [Bug-gmx_MMPBSA]: gmx_MMPBSA does not support water/ions molecules in any structure
Issue -
State: open - Opened by Howpow88 4 months ago
- 1 comment
#500 - [Bug-gmx_MMPBSA]: IndexError: list index out of range
Issue -
State: closed - Opened by RazzyChen 4 months ago
- 3 comments
#499 - IEEE_DIVIDE_BY_ZERO error
Issue -
State: open - Opened by LAndersen1 5 months ago
- 3 comments
#498 - [Question]: How to restart the PBSA/GBSA
Issue -
State: closed - Opened by ssagar61 5 months ago
- 1 comment
#496 - [Bug-gmx_MMPBSA]: prmtop error
Issue -
State: open - Opened by overlord1647 5 months ago
- 3 comments
#495 - [Bug-gmx_MMPBSA]: mmbgsa fails at "Parsing results to output files..." stage
Issue -
State: closed - Opened by morin-andrew 5 months ago
- 10 comments
#493 - Corrected _temp_top.top behaviour to accommodate asynchronous scenarios
Pull Request -
State: closed - Opened by ale94mleon 5 months ago
- 5 comments
#492 - [Bug-gmx_MMPBSA]: Different version of Gromacs was incompatible with gmxMMPBSA
Issue -
State: closed - Opened by yesyb 5 months ago
- 1 comment
#491 - [Bug-gmx_MMPBSA_ana]:
Issue -
State: open - Opened by snehachem 5 months ago
- 1 comment
#489 - [Bug-gmx_MMPBSA]: The atom 6719 in the complex index is not found in the topology file. Please check that the files are consistent.
Issue -
State: closed - Opened by jjjjjqt 5 months ago
- 4 comments
#488 - Updating the versioneering library
Pull Request -
State: closed - Opened by LAndersen1 5 months ago
- 1 comment
#487 - [Bug-gmx_MMPBSA]: Update for versioneer required to pip install master branch
Issue -
State: closed - Opened by LAndersen1 5 months ago
#486 - Fixing get_corrstd for small system changes
Pull Request -
State: closed - Opened by LAndersen1 5 months ago
- 1 comment
#485 - [Bug-gmx_MMPBSA]: get_corrstd fails for val1=4529748.935791228 and val2=4529748.938629
Issue -
State: closed - Opened by LAndersen1 5 months ago
#484 - [Bug-gmx_MMPBSA]:
Issue -
State: closed - Opened by debanjansen48 6 months ago
- 6 comments
#483 - [Bug-gmx_MMPBSA]: gmx_MMPBSA does not support water/ions molecules in any structure, but we found 113 molecules in the complex
Issue -
State: open - Opened by Premanandabasak 6 months ago
- 6 comments
#481 - GromacsError: Structure contains XXX molecules, but no template defined
Issue -
State: closed - Opened by josephDeluna 6 months ago
- 7 comments
#480 - [Question]: Error pdb4amber: No module named parmed
Issue -
State: closed - Opened by A-Sethi 6 months ago
- 1 comment
#479 - [Bug-gmx_MMPBSA]: The complex index has fewer atoms than the topology. Please check that the files are consistent.
Issue -
State: open - Opened by ChenHiuhong1 6 months ago
- 17 comments
#478 - [Question]: The reason why different outcomes happen when I extract adjacent time to calculate the binding affinity.
Issue -
State: closed - Opened by allanlinzhang 6 months ago
- 3 comments
#477 - Financial and support
Issue -
State: open - Opened by Valdes-Tresanco-MS 6 months ago
Labels: announcement
#476 - [Bug-gmx_MMPBSA]: pb_fdfrc(): Atom out of focusing box
Issue -
State: closed - Opened by lachrymator 6 months ago
- 10 comments
Labels: unsupported force field, A coffee ☕
#475 - [Bug-gmx_MMPBSA]: cpptraj generate empty mdcrd
Issue -
State: open - Opened by jsjyhzy 6 months ago
- 1 comment
Labels: bug
#473 - [Question]: How to download gmx_MMPBSA_ana on Windows ?
Issue -
State: closed - Opened by allanlinzhang 7 months ago
- 2 comments
#472 - [Bug-gmx_MMPBSA]:
Issue -
State: closed - Opened by lachrymator 7 months ago
- 2 comments
#471 - [Question]: About the Force Fileds
Issue -
State: closed - Opened by allanlinzhang 7 months ago
- 1 comment
#470 - why ΔEPB in output results is 0
Issue -
State: closed - Opened by ProteinCamera 7 months ago
- 4 comments
#469 - [Bug-gmx_MMPBSA]: TypeError: string indices must be integers, not 'str'
Issue -
State: closed - Opened by allanlinzhang 7 months ago
- 8 comments
Labels: wrong-groups
#468 - [Bug-gmx_MMPBSA_ana]: pandas._config.config.OptionError: "No such keys(s): 'mode.use_inf_as_null'"
Issue -
State: open - Opened by camattelaer 7 months ago
- 3 comments
#467 - MMPBSA——index error: list index out of range
Issue -
State: closed - Opened by HariniSureshKumar 7 months ago
- 8 comments
#465 - [Bug-gmx_MMPBSA]: TypeError('Cannot translate exceptions')
Issue -
State: closed - Opened by WoutVanEynde 7 months ago
- 8 comments
#464 - [Bug-gmx_MMPBSA]: .gro not possible for -cs
Issue -
State: closed - Opened by WoutVanEynde 7 months ago
- 1 comment
#463 - TypeError: string indices must be integers
Issue -
State: closed - Opened by kratos1459 7 months ago
- 1 comment
#462 - gmx_MMPBSA: Protein-ligand free energy calculation error
Issue -
State: closed - Opened by sajqazi 7 months ago
- 6 comments
Labels: topology
#461 - [Question]: list index out of range error?
Issue -
State: closed - Opened by Baluxy 7 months ago
- 5 comments
#460 - [Bug-gmx_MMPBSA]: error when converting gromacs topology to amber topology
Issue -
State: closed - Opened by WoutVanEynde 7 months ago
- 4 comments
#459 - [Question]: How to fix IndexError : list index out of range
Issue -
State: closed - Opened by Poowad 8 months ago
- 7 comments
#458 - [ENH]: Support for QM/MM simulations with QUICK
Issue -
State: open - Opened by marioernestovaldes 8 months ago
Labels: enhancement, xbfree
#457 - [Bug-gmx_MMPBSA_test]: ModuleNotFoundError: No module named 'parmed'
Issue -
State: closed - Opened by alanjchang 8 months ago
- 3 comments
#456 - [Doc]: MMPBSA_Error: Could not find necessary program [tleap]
Issue -
State: closed - Opened by sajqazi 8 months ago
- 1 comment
#455 - [Bug-gmx_MMPBSA]: The number of atoms in the topology and the complex structure are different
Issue -
State: closed - Opened by Aunity 9 months ago
- 9 comments
#454 - [ENH]: qm atom mask selection
Issue -
State: open - Opened by camattelaer 9 months ago
- 11 comments
Labels: enhancement
#453 - [Question]: positive ΔG binding
Issue -
State: open - Opened by niloufar1993 9 months ago
- 3 comments
#452 - [Question]: how can I get ΔTOTAL and ΔG binding in the output file?
Issue -
State: closed - Opened by niloufar1993 9 months ago
- 2 comments
#451 - [Question]: MMPBSA_Error: Could not find necessary program [sander.APBS]
Issue -
State: closed - Opened by fatih4534 9 months ago
- 4 comments
#450 - [Bug-gmx_MMPBSA]: KeyError: 'temperature' when calculating QH entropy
Issue -
State: closed - Opened by camattelaer 9 months ago
- 6 comments
#449 - [Question]: How to calculate GB
Issue -
State: closed - Opened by Admire7494 9 months ago
- 4 comments
#448 - Install gmx_MMPBSA in HPC
Issue -
State: open - Opened by yuqingxiong96 9 months ago
- 2 comments
#447 - TypeError: ChamberParm does not support all potential terms defined in the input Structure
Issue -
State: closed - Opened by rodrisantiago 9 months ago
- 6 comments
#446 - [Question]: using native AMBER files
Issue -
State: closed - Opened by camattelaer 9 months ago
- 2 comments
#445 - GromacsError: Only 3-point vsite type 1 is supported
Issue -
State: closed - Opened by yuqingxiong96 9 months ago
- 2 comments
#442 - [Question]: Why is my △TOTAL positive?
Issue -
State: open - Opened by yuqingxiong96 10 months ago
- 10 comments
#441 - The atom xxx in the complex index is not found in the topology file
Issue -
State: closed - Opened by whimouse 10 months ago
- 3 comments
#438 - [Question]: My molecule has two parts, A and B. I want to calculate the interaction between AB, but I don't want to consider the AB interaction within the same molecule. What should I do
Issue -
State: open - Opened by kkivg 10 months ago
- 2 comments
#435 - [Question]: How to calculate the entropy of protein-protein system using gmx_MMPBSA?
Issue -
State: closed - Opened by Ishrat-Jahan1 10 months ago
- 15 comments
#433 - [Question]: Does gmx_mmpbsa support GROMOS force fields?
Issue -
State: closed - Opened by kkivg 10 months ago
- 1 comment
Labels: gromos
#432 - [Bug-gmx_MMPBSA_ana]: qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found
Issue -
State: open - Opened by WANJIAL 11 months ago
- 1 comment
#431 - [Question]: MMPBSA_Error: Selecting residue A:GLY:76 can't be mutated. Please, define a valid residue...
Issue -
State: closed - Opened by zengdashi 11 months ago
- 5 comments
#430 - [Question]: I have meet a problem about IndexError: string index out of range
Issue -
State: closed - Opened by zengdashi 11 months ago
- 2 comments
#429 - [Bug-gmx_MMPBSA]: PC crashes when running with mpirun
Issue -
State: closed - Opened by avinashkarkada 11 months ago
- 2 comments
#428 - gmx_MMPBSA_ana unexpectedly closes
Issue -
State: closed - Opened by drbipinraj 12 months ago
- 4 comments
Labels: third-party package
#427 - [Bug-gmx_MMPBSA]: gmx make_ndx failed when querying index.ndx
Issue -
State: closed - Opened by Tamer-12345 12 months ago
- 2 comments
#426 - [ENH]: Decomp option to show only ligand-receptor interactions
Issue -
State: open - Opened by wrmartin 12 months ago
- 1 comment
Labels: enhancement
#425 - [Question]: How is the decomposition cut-off radius calculated?
Issue -
State: closed - Opened by WoutVanEynde 12 months ago
- 1 comment
#424 - [Question]: gmx trjconv failed when querying com_traj.xtc
Issue -
State: closed - Opened by wyplogin 12 months ago
- 5 comments
#423 - [Bug-gmx_MMPBSA]: gmx make_ndx failed when querying index_LIG.ndx
Issue -
State: closed - Opened by dj8207 12 months ago
- 5 comments