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About pmx: Automated protein structure and topology generation for alchemical perturbations
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0
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1590
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June 10, 2016
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Absolute binding Free energy with NE-MD: Single-step complex leg & Boresch restraint tips
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1
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25
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August 4, 2025
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Issue in Probability distribution overlap for D2E transformation
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8
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30
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July 4, 2025
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Challenges in Reproducing ddG Estimation Results for 1STN
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28
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395
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June 5, 2025
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Mutation free energy calculation for protein membrane interaction
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2
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28
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May 19, 2025
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Repeatability of state A to State B alchemical transformation
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2
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31
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April 17, 2025
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PMX alchemical free energy calculation for protein mutation
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1
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38
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March 25, 2025
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Pmx ligandHybrid error
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7
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61
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March 15, 2025
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PMX Ligand Preparation from Scratch - Atom Types and Parameter Discrepancies
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2
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47
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February 28, 2025
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Error with pmx and openforcefield generated files
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1
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47
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January 27, 2025
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Pmx and CHARM36 using output from CGenFF server
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3
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35
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January 20, 2025
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Pmx analyse says "no good dgdl files provided"
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2
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19
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January 13, 2025
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Installation Problem of PMX
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12
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97
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January 13, 2025
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Help request protein-ligand tutorial error fix
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8
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55
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December 30, 2024
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Help with Charged Ligand Non-Equilibrium Free Energy Calculations Using Co-Alchemical Ion Approach
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3
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55
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December 20, 2024
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Relative constraint deviation after LINCS
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15
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2211
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December 9, 2024
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LINCS warning and segmentation fault @ non-equilibrium part of simulation
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7
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65
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December 9, 2024
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PMX AssertionError, Atom type OH not been defined in the force field, Atom DHD1 was not found
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3
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41
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November 13, 2024
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After running the ddG calculation tutorial (ligand_tutorial.ipynb), I got different result
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7
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69
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October 28, 2024
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Non-standard amino acid mutation - dihedrals error
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2
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59
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September 25, 2024
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Is the pmx web-server OK?
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1
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26
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September 25, 2024
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Pmx and protein structure water molecules
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2
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66
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May 24, 2024
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Error in AtomMapping with more than 100 atoms
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2
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81
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April 4, 2024
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Pmx error pmx mutate -f protein.pdb -o mutant.pdb
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1
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186
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March 6, 2024
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'ligandHybrid' ERROR: fitting mol2 on mol1 failed
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4
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179
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February 21, 2024
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LINCS constraints all bonds to h-bonds only
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7
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142
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February 16, 2024
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Error with 'make_hybrid.py' Using CGenFF
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4
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150
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February 12, 2024
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Issue with pdb2gmx and charm36mut forcefield: Undefined Atom Type "OH"
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4
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358
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December 7, 2023
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Make_hybrid.py list index out of range error
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14
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1141
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December 4, 2023
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Questions on Non-equilibrium TI Phase with Slurm Scheduler in 'AZtutorial.py' Script
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2
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200
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December 4, 2023
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