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Does bond order in MOL2 file affect rtp generation and pdb2gmx?
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2
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21
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June 5, 2025
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Confusion over RB and Fourier Dihedrals
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0
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9
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May 29, 2025
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Apply constraints to desire molecules
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3
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28
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March 28, 2025
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Novice to simulate antibody-drug-conjugate -- unnatural residues
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1
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22
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March 26, 2025
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cGenFF Ligand topology
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0
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62
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March 13, 2025
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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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25
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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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37
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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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82
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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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70
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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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42
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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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83
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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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1358
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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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54
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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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178
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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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87
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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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31
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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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33
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September 26, 2024
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Protein with Ion cofactors
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1
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29
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September 6, 2024
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Topology files with packmol
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5
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551
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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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108
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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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30
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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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54
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July 7, 2024
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.gro no match .top
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3
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32
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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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378
|
July 4, 2024
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Problem with chain definition, or missing terminal residues
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1
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161
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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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102
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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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57
|
June 19, 2024
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MARTINI Parameters for DMG (1,2-Dimyristoyl-rac-glycerol)
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1
|
75
|
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
|
114
|
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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363
|
May 5, 2024
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