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About pmx: Automated protein structure and topology generation for alchemical perturbations
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0
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1621
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June 10, 2016
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NVT vs NPT for Non-Equilibrium Switching in pmx/GROMACS
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1
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24
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January 26, 2026
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Using PMX for ΔΔG on a glycosylated Fc (P238D back-mutation; PDB 3WJJ): viable workflows?
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5
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67
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November 20, 2025
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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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93
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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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55
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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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579
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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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68
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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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57
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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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84
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March 25, 2025
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Pmx ligandHybrid error
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7
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108
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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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76
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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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73
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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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74
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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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37
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January 13, 2025
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Installation Problem of PMX
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12
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177
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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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96
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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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116
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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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2268
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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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123
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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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63
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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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107
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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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73
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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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34
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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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82
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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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94
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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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197
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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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211
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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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165
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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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170
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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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412
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December 7, 2023
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