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How to add hydrogen atoms to the complex with correct coordinates?
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2
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15
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January 23, 2026
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Pdb2gmx rounds up the charge of a single atom
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7
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32
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January 21, 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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How to add terminal caps in AMBER with GROMACS
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1
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54
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December 3, 2025
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How to include bound calcium in amylase structure
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4
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41
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November 21, 2025
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Error Query Regarding pdb2gmx Generating TOP Files Containing DNA Fragments
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1
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32
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November 15, 2025
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Pdb2gmx not recognizing water block
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1
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36
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November 11, 2025
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How to setup protein-ligand simulation using CHARMM-GUI for ligand preparation
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9
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252
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October 26, 2025
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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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GROMACS 2025.3 CUDA 13 RTX 5070 Ti Fails on Simulations
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2
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86
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October 14, 2025
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what should do with zink-protein.pdf to get topology file?
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5
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55
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October 7, 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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How to deal with protonation state in GROMACS? (encountering fatal error)
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4
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125
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September 29, 2025
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CNT creation having more than 999 atoms
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3
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49
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September 19, 2025
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The amino acids reported as errors by pdb2gmx do not correspond to the amino acids in the structure
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1
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15
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September 19, 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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Question about Changing DNA residues to Protein in residuetypes.dat for covalent bond
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1
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22
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August 4, 2025
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Why Does GROMACS Rename a DG Terminus to DG5 Without Manual Patching?
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0
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22
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July 22, 2025
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Homocysteine covalently bonded with a protein MD simulation how to perform
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0
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40
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July 21, 2025
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Pdb2gmx: -ter option doesn't work
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1
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73
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July 16, 2025
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How to create restrained file for sol
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0
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21
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July 15, 2025
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Potential bug in pdb2gmx
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1
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46
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May 20, 2025
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System has non-zero total charge: -1.000000
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1
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37
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May 19, 2025
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Fatal error: Residue 175 named GLU of a molecule in the input file was mapped to an entry in the top
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0
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37
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May 18, 2025
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Atom C1 not found in building block 1MET while combining tbp and trp
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0
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80
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May 18, 2025
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How to simulate d-amino acids
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10
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449
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March 8, 2025
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Issue with pdb2gmx with MT-COX2 gene
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0
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32
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February 27, 2025
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Inconsistency in user input: Could not find force field 'martini3.ff' in current directory, install
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0
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81
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February 24, 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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Adding a new residue covalently linked to multiple cysteines
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0
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43
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February 6, 2025
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