Valdes-Tresanco-MS/gmx_MMPBSA issues and pull requests

#564 - KeyError: 'delta' while running gmx_MMPBSA_ana

Issue - State: open - Opened by accibio 18 days ago - 4 comments

#563 - [Bug-gmx_MMPBSA]: Atom Order Mismatch in gmx_MMPBSA with a Glycan-Containing System

Issue - State: open - Opened by mohamedmarzouk22 21 days ago - 2 comments

#562 - [Bug-gmx_MMPBSA]: Compilation warnings regarding regular expression

Issue - State: open - Opened by markus-meier74 29 days ago - 3 comments

#556 - [Question]: bad atom type: Pb and sander failed with prmtop COM.prmtop!

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

#551 - [Bug-gmx_MMPBSA]: installation issue

Issue - State: closed - Opened by snehachem 3 months ago - 9 comments

#550 - Fix typo

Pull Request - State: closed - Opened by tikuta 3 months ago - 1 comment

#549 - [Question]: ERROR HELP

Issue - State: closed - Opened by mkoiral 3 months ago - 15 comments

#548 - [Bug-gmx_MMPBSA_ana]:

Issue - State: open - Opened by Jackshoulder 3 months ago

#547 - [Question]: Impact of ionic strength in MMPBSA calculations

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

#545 - [Question]: a question. When do Decomposition analysis, selected some residues, but gmx_MMPBSA_ana do not show all of them.

Issue - State: closed - Opened by guoshi22 3 months ago - 2 comments

#543 - [Question]: running MMPBSA by gromos forcefield toplogy and gromacs 2023.2

Issue - State: closed - Opened by benyamin-moraditabar 4 months ago - 4 comments

#541 - [Bug-gmx_MMPBSA]: The Topology's File Process Is Wrong

Issue - State: open - Opened by linjiahao962889027 4 months ago - 1 comment
Labels: bug

#540 - [Bug-gmx_MMPBSA]: gmx_MMPBSA does not support water/ions molecules in any structure, but we found 2 molecules in the complex

Issue - State: open - Opened by yyf2626 4 months ago - 3 comments

#539 - [Question]: having index error with assigning chain ID.

Issue - State: closed - Opened by tjrong123 5 months ago - 3 comments

#537 - [Bug-gmx_MMPBSA]: sander failed with prmtop COM.prmtop!

Issue - State: open - Opened by dxf320 5 months ago - 9 comments

#536 - [Question]: Which file was used to create index.ndx file for binding energay caluclation?

Issue - State: closed - Opened by Tangbbmc 5 months ago - 6 comments

#535 - [Bug-gmx_MMPBSA_ana]: Analysis with QH runs prevent GUI analysis

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

#534 - test

Issue - State: closed - Opened by Samuel-gwb 6 months ago

#533 - [Bug-gmx_MMPBSA_ana]: Could not import PyQt5/PyQt6

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

#532 - Update env.yml

Pull Request - State: closed - Opened by pritampanda15 6 months ago

#531 - [Doc]: Alanine Scann issue

Issue - State: closed - Opened by julruiz72 6 months ago - 1 comment

#530 - [Bug-gmx_MMPBSA]: Failed building wheel for pandas

Issue - State: closed - Opened by hubertrybka 6 months ago - 2 comments

#529 - [Bug-gmx_MMPBSA]: failed with prmtop COM.prmtop!

Issue - State: open - Opened by Simon-dumplings 7 months ago

#528 - [Bug-gmx_MMPBSA]:

Issue - State: closed - Opened by JuuelHerza 7 months ago - 8 comments

#526 - [Bug-gmx_MMPBSA]: ImportError with mpi4py

Issue - State: closed - Opened by jstump-1999 7 months ago - 4 comments

#524 - [Bug-gmx_MMPBSA]: teLeap Error

Issue - State: open - Opened by mkoiral 7 months ago - 30 comments

#523 - [Question]: Error: The complex, receptor, and ligand trajectories must be the same length.

Issue - State: open - Opened by alanrodriguez06 7 months ago - 1 comment
Labels: bug

#522 - [Question]: GromacsError: Only 3-point vsite type 1 is supported

Issue - State: open - Opened by huaiaee 7 months ago - 7 comments

#521 - [Questunable to get the decomposition result

Issue - State: closed - Opened by suruchi-25 7 months ago - 6 comments

#520 - [Bug-gmx_MMPBSA]:

Issue - State: closed - Opened by suruchi-25 7 months ago - 2 comments

#519 - [Issue-gmx_MMPBSA]: IndexError: list index out of range

Issue - State: closed - Opened by Ossmonde 7 months ago - 1 comment

#518 - [Question]: unable to understand the results

Issue - State: open - Opened by suruchi-25 7 months ago - 8 comments

#517 - [Question]: I am not able to install gmxmmpbsa on ubuntu 2024.

Issue - State: open - Opened by AKR845 8 months ago - 13 comments

#516 - [Bug-gmx_MMPBSA_ana]:KeyError : "delta"

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

#515 - Installing gmx_MMPBSA on HPC using AmberTools method

Issue - State: closed - Opened by ocampbel 8 months ago - 5 comments

#514 - [Bug-gmx_MMPBSA]:

Issue - State: closed - Opened by suruchi-25 8 months ago - 4 comments

#513 - [Bug-gmx_MMPBSA_ana]: can not open gmx_MMPBSA_ana

Issue - State: open - Opened by jackhu5 8 months ago - 3 comments

#512 - [Bug-gmx_MMPBSA]: PyQt6/QtGui.abi3.so: undefined symbol: _ZN5QFont11tagToStringEj, version Qt_6

Issue - State: closed - Opened by suruchi-25 9 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 9 months ago - 1 comment

#510 - [Bug-gmx_MMPBSA]: TypeError: string indices must be integers

Issue - State: closed - Opened by suruchi-25 9 months ago - 7 comments

#509 - [Bug-gmx_MMPBSA]: gmx_MMPBSA: error: unrecognized arguments

Issue - State: closed - Opened by suruchi-25 9 months ago - 1 comment

#508 - [Question]: Handling Protein-Ligand Complexes Embedded in Membranes with LPH Atoms

Issue - State: closed - Opened by huaiaee 9 months ago - 5 comments

#507 - [Question]: Energy differences between WT and mutation

Issue - State: open - Opened by WoutVanEynde 9 months ago - 3 comments

#506 - [Question]: The results of multiple calculations are exactly the same

Issue - State: closed - Opened by chanchanchanchanchan 9 months ago - 9 comments

#505 - [Question: Building Normal Complex Amber Topology Error

Issue - State: open - Opened by lvckyv 9 months ago - 2 comments

#504 - [Question]: TypeError in res2map When Running Protein-Ligand Binding Free Energy Calculations

Issue - State: closed - Opened by huaiaee 9 months ago - 7 comments

#503 - [Question]: Facing trouble with mmpbsa sander and PB calculation for protein-ligand complex

Issue - State: open - Opened by Rajath701 9 months ago - 13 comments

#502 - [Question]: How to calculate the binding free energy of lipids membrane and peptide

Issue - State: closed - Opened by chanchanchanchanchan 9 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 9 months ago - 1 comment

#500 - [Bug-gmx_MMPBSA]: IndexError: list index out of range

Issue - State: closed - Opened by RazzyChen 9 months ago - 3 comments

#499 - IEEE_DIVIDE_BY_ZERO error

Issue - State: open - Opened by LAndersen1 9 months ago - 3 comments

#498 - [Question]: How to restart the PBSA/GBSA

Issue - State: closed - Opened by ssagar61 9 months ago - 1 comment

#496 - [Bug-gmx_MMPBSA]: prmtop error

Issue - State: open - Opened by overlord1647 10 months ago - 3 comments

#495 - [Bug-gmx_MMPBSA]: mmbgsa fails at "Parsing results to output files..." stage

Issue - State: closed - Opened by morin-andrew 10 months ago - 10 comments

#493 - Corrected _temp_top.top behaviour to accommodate asynchronous scenarios

Pull Request - State: closed - Opened by ale94mleon 10 months ago - 5 comments

#492 - [Bug-gmx_MMPBSA]: Different version of Gromacs was incompatible with gmxMMPBSA

Issue - State: closed - Opened by yesyb 10 months ago - 1 comment

#491 - [Bug-gmx_MMPBSA_ana]:

Issue - State: open - Opened by snehachem 10 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 10 months ago - 4 comments

#488 - Updating the versioneering library

Pull Request - State: closed - Opened by LAndersen1 10 months ago - 1 comment

#487 - [Bug-gmx_MMPBSA]: Update for versioneer required to pip install master branch

Issue - State: closed - Opened by LAndersen1 10 months ago

#486 - Fixing get_corrstd for small system changes

Pull Request - State: closed - Opened by LAndersen1 10 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 10 months ago

#484 - [Bug-gmx_MMPBSA]:

Issue - State: closed - Opened by debanjansen48 10 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 10 months ago - 6 comments

#481 - GromacsError: Structure contains XXX molecules, but no template defined

Issue - State: closed - Opened by josephDeluna 11 months ago - 7 comments

#480 - [Question]: Error pdb4amber: No module named parmed

Issue - State: closed - Opened by A-Sethi 11 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: closed - Opened by ChenHiuhong1 11 months ago - 22 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 11 months ago - 3 comments

#477 - Financial and support

Issue - State: open - Opened by Valdes-Tresanco-MS 11 months ago
Labels: announcement

#476 - [Bug-gmx_MMPBSA]: pb_fdfrc(): Atom out of focusing box

Issue - State: closed - Opened by lachrymator 11 months ago - 10 comments
Labels: unsupported force field, A coffee ☕

#475 - [Bug-gmx_MMPBSA]: cpptraj generate empty mdcrd

Issue - State: open - Opened by jsjyhzy 11 months ago - 1 comment
Labels: bug

#473 - [Question]: How to download gmx_MMPBSA_ana on Windows ?

Issue - State: closed - Opened by allanlinzhang 11 months ago - 2 comments

#472 - [Bug-gmx_MMPBSA]:

Issue - State: closed - Opened by lachrymator 11 months ago - 2 comments

#471 - [Question]: About the Force Fileds

Issue - State: closed - Opened by allanlinzhang 11 months ago - 1 comment

#470 - why ΔEPB in output results is 0

Issue - State: closed - Opened by ProteinCamera 12 months ago - 4 comments

#469 - [Bug-gmx_MMPBSA]: TypeError: string indices must be integers, not 'str'

Issue - State: closed - Opened by allanlinzhang 12 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 12 months ago - 3 comments

#467 - MMPBSA——index error: list index out of range

Issue - State: closed - Opened by HariniSureshKumar 12 months ago - 8 comments

#465 - [Bug-gmx_MMPBSA]: TypeError('Cannot translate exceptions')

Issue - State: closed - Opened by WoutVanEynde 12 months ago - 8 comments

#464 - [Bug-gmx_MMPBSA]: .gro not possible for -cs

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

#463 - TypeError: string indices must be integers

Issue - State: closed - Opened by kratos1459 12 months ago - 1 comment

#462 - gmx_MMPBSA: Protein-ligand free energy calculation error

Issue - State: closed - Opened by sajqazi about 1 year ago - 6 comments
Labels: topology

#461 - [Question]: list index out of range error?

Issue - State: closed - Opened by Baluxy about 1 year ago - 5 comments

#460 - [Bug-gmx_MMPBSA]: error when converting gromacs topology to amber topology

Issue - State: closed - Opened by WoutVanEynde about 1 year ago - 4 comments

#459 - [Question]: How to fix IndexError : list index out of range

Issue - State: closed - Opened by Poowad about 1 year ago - 7 comments

#458 - [ENH]: Support for QM/MM simulations with QUICK

Issue - State: open - Opened by marioernestovaldes about 1 year ago
Labels: enhancement, xbfree

#457 - [Bug-gmx_MMPBSA_test]: ModuleNotFoundError: No module named 'parmed'

Issue - State: closed - Opened by alanjchang about 1 year ago - 3 comments

#456 - [Doc]: MMPBSA_Error: Could not find necessary program [tleap]

Issue - State: closed - Opened by sajqazi about 1 year 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 about 1 year ago - 9 comments

#454 - [ENH]: qm atom mask selection

Issue - State: open - Opened by camattelaer about 1 year ago - 11 comments
Labels: enhancement

#453 - [Question]: positive ΔG binding

Issue - State: open - Opened by niloufar1993 about 1 year ago - 3 comments

#452 - [Question]: how can I get ΔTOTAL and ΔG binding in the output file?

Issue - State: closed - Opened by niloufar1993 about 1 year ago - 2 comments

#451 - [Question]: MMPBSA_Error: Could not find necessary program [sander.APBS]

Issue - State: closed - Opened by fatih4534 about 1 year ago - 4 comments

#450 - [Bug-gmx_MMPBSA]: KeyError: 'temperature' when calculating QH entropy

Issue - State: closed - Opened by camattelaer about 1 year ago - 6 comments

#449 - [Question]: How to calculate GB

Issue - State: closed - Opened by Admire7494 about 1 year ago - 4 comments

#448 - Install gmx_MMPBSA in HPC

Issue - State: open - Opened by yuqingxiong96 about 1 year ago - 2 comments

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