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How to set the bond constraint of the sidechain in a self-designed peptide
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3
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15
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February 18, 2025
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How to perform md simulation on a protein structure which have a ca+ ions
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0
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14
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January 23, 2025
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Chloroform as a solvent in Charmm36 force field
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1
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38
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January 16, 2025
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Issues with Ligand Topology Creation Using CGENFF and CHARMM-GUI
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2
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39
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January 7, 2025
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Atom OXT in residue GLN 336 was not found in rtp entry GLN with 17 atoms while sorting atoms
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3
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27
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December 19, 2024
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High Penalty Score in CGENFF topology
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0
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34
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December 15, 2024
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Fatal error: number of coordinates in coordinate file does not match topology file
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4
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1090
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December 9, 2024
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Applying constraints to different molecules in a same system
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0
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41
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November 19, 2024
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Trouble with CGenFF and Ligand Topology in GROMACS
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0
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115
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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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49
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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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22
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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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18
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September 26, 2024
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Protein with Ion cofactors
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1
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21
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September 6, 2024
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Topology files with packmol
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5
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438
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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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73
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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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24
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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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49
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July 7, 2024
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.gro no match .top
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3
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29
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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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281
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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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116
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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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91
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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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56
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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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69
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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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111
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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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327
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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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118
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April 26, 2024
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Topology versus initial configuration
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2
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64
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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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194
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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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127
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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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188
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February 28, 2024
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