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Pdb2gmx fails: Residue 'MGP' not found in CHARMM36 force field
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1
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15
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August 9, 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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13
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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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15
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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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27
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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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37
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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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18
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July 15, 2025
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Potential bug in pdb2gmx
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1
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29
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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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27
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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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12
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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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55
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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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273
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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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23
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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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60
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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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26
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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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30
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February 6, 2025
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Pdb2gmx not able to form bonds in an unusual ligand
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5
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80
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January 30, 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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44
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January 23, 2025
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Topology of an ACE-linked cyclic peptide with a free C-ter
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0
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43
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January 23, 2025
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Parametrization of DNA Backbone with Alkyl Chain Using CHARM and Non-Integer Charge Issue
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0
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13
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January 22, 2025
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Position restraints missing when .itp is printed to .top
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2
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69
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January 21, 2025
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Inserting a modified residue into a protein/DNA chain using pdb2gmx
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34
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1743
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December 27, 2024
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Fatal error atom C2 not found in buiding block 166MET while combining tdb and rtp
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1
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57
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December 21, 2024
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Pdb2gmx residues in the chain do not have consistent type. Simulated protein contains D-amino acids
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5
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114
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December 18, 2024
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Error: Topol.top file doesn`t match solv.gro file
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1
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68
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December 18, 2024
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gmx_MMPBSA order of the molecules in the pdb file and topology file
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0
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25
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December 17, 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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1445
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December 9, 2024
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CGenFF ERROR - attype warning: unknown sulfur type (SD) not supported; skipped molecule
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1
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180
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December 4, 2024
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Atom Type Error in Gromacs
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0
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20
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December 3, 2024
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Pdb2gmx error: atom CB used in topology entry is not found in the input file
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1
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60
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November 30, 2024
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Pdb/topology file for transition metal oxides for supercapacitor MD simulation
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0
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17
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November 25, 2024
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