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How to build Ligand topology
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0
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8
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January 23, 2026
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Fatal error: number of coordinates in coordinate file does not match topology file
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7
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1698
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January 7, 2026
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Topology files with packmol
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6
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698
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October 20, 2025
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Pdb2gmx fails: Residue 'MGP' not found in CHARMM36 force field
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2
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59
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October 5, 2025
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x2top for MINFF
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0
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56
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October 2, 2025
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How to generate topology and .itp files for succinic acid and Zn²⁺ in GROMACS using OPLS-AA?
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0
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35
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August 28, 2025
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Modifying topol.top with each step of peptide insertion over membrane from CHARMM-GUI
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2
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71
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August 2, 2025
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Does bond order in MOL2 file affect rtp generation and pdb2gmx?
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2
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54
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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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32
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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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46
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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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37
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March 26, 2025
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cGenFF Ligand topology
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0
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113
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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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36
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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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71
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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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152
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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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121
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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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67
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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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134
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December 15, 2024
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Applying constraints to different molecules in a same system
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0
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72
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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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226
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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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144
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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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68
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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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58
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September 26, 2024
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Protein with Ion cofactors
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1
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48
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September 6, 2024
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Issues Running GROMACS with Amber Force Field - Seeking Guidance
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1
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160
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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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49
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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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81
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July 7, 2024
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.gro no match .top
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3
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64
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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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504
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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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235
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June 25, 2024
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