About pmx: Automated protein structure and topology generation for alchemical perturbations
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0
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1284
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June 10, 2016
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Oscillational period warning during tripeptide A2I forward simulation
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12
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75
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January 24, 2023
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Problem in using gentop
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12
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24
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January 20, 2023
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List index out of range when running pmx gentop
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2
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47
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December 29, 2022
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Understanding the options of atom mapping and ligandHybrid
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3
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40
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December 21, 2022
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Bonds that rotated more than 30 degrees:
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1
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81
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November 3, 2022
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IndexError: list index out of range while preparing pdb file
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1
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152
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September 15, 2022
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Problem with installing with Python2
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9
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77
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September 7, 2022
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Ligand topolgies for pmx
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5
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143
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September 1, 2022
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Pmx RBFE gives oddly large deltaG
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1
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86
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August 14, 2022
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PMX engineered resiude
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4
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104
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July 18, 2022
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Pmx ABFE ligand only simulation set-up
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3
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125
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July 18, 2022
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Using pmx genlib and hybrid topologies
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3
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142
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July 11, 2022
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PMX generating protein ligand simulation system with Charmm/cgenff forcefields
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1
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142
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June 14, 2022
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Free energy calculations error
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1
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348
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June 14, 2022
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Free Energy Calculation: State B has non-zero total charge: -1.000000
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1
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138
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June 14, 2022
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Free energy calculation with double system/single box simulation
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12
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219
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March 30, 2022
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Error with Zn atom
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3
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160
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March 29, 2022
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Problem with SS bridges - Bug?
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3
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147
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March 24, 2022
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Peptide Nucleic Acid Functionality
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2
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187
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January 2, 2022
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Pmx - problems reproducing benchmarking from de Groot 2020
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2
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293
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October 17, 2021
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Itp ligand file generation
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3
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515
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October 14, 2021
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A non-finite potential energy in non-equilibrium transition with pmx
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2
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285
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October 1, 2021
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Alchemical free energy calculations
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1
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255
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October 1, 2021
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LINCS error during Alchemical free energy calculation
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1
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273
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September 30, 2021
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Energy minimization of hybrid ligand
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2
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372
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November 13, 2020
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Relative constraint deviation after LINCS
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6
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1268
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October 9, 2020
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Dual Topology Generator for Alchemical Pathways
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1
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590
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October 9, 2020
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Make_hybrid.py list index out of range error
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2
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456
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October 9, 2020
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Installed - can't import _pmx as _p
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3
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680
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July 4, 2020
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