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Trouble with CGenFF and Ligand Topology in GROMACS
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0
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23
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October 19, 2024
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Help with "Inconsistent Residue Types" Error
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1
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22
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September 30, 2024
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Error in using cgenff for ligand topology, ligand.str missed bond information
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1
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12
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September 27, 2024
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Error in CGenFF: "No valid resonance structure found"
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3
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13
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September 26, 2024
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Protein with Ion cofactors
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1
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13
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September 6, 2024
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Topology files with packmol
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5
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359
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September 4, 2024
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Issues Running GROMACS with Amber Force Field - Seeking Guidance
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1
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37
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August 26, 2024
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Problem in generating topology file for nanoporous MoS2 membrane
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0
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20
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July 10, 2024
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Topol.top file not generating
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1
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40
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July 7, 2024
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.gro no match .top
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3
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27
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July 5, 2024
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Build the Topology (adding .prm and .itp)
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3
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192
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July 4, 2024
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Problem with chain definition, or missing terminal residues
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1
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81
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June 25, 2024
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How to add new residue in the lipids.rtp in charmm27.ff?
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6
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73
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June 20, 2024
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How define phosphoaspartate in Charmm36?
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3
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52
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June 19, 2024
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MARTINI Parameters for DMG (1,2-Dimyristoyl-rac-glycerol)
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1
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63
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June 14, 2024
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Residue 1 named ALA of a molecule in the input file was mapped to an entry in the topology database
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0
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108
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May 6, 2024
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Incorrect relative solvation free energy values using single topology alchemical transformation
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8
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295
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May 5, 2024
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Difference between x2top and LigParGen ff generation (dodecane)
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1
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111
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April 26, 2024
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Topology versus initial configuration
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2
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63
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April 25, 2024
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Extrapolating LJ14 and Coul 14 entries from LJ (SR) and Coul (SR) when [ pairs_nb ] is used
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0
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172
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March 15, 2024
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Ligand Topoly for GROMOS 96
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0
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117
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March 6, 2024
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Why do we call topology files 'topology'?
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2
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183
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February 28, 2024
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MD of ionic supramolecular complex
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1
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161
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February 20, 2024
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Fatal error: number of coordinates in coordinate file does not match topology file
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2
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852
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February 3, 2024
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Error in user input: Required option was not provided, and the default file 'topol' does not exist
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3
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228
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February 1, 2024
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Small rigid molecules with constraints
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4
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358
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December 10, 2023
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Regarding the topology is not created in the ATB server. how to overcome this issue?
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0
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184
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December 1, 2023
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Help with Multiplicity in Improper Dihedrals
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2
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414
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November 15, 2023
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Error in NPT
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6
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332
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November 9, 2023
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Helix unfolding despite position restraints
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0
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199
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November 7, 2023
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