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How to create restrained file for sol
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0
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4
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July 15, 2025
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Pdb2gmx: -ter option doesn't work
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0
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19
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May 26, 2025
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Potential bug in pdb2gmx
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1
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27
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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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25
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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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11
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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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52
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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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249
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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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21
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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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53
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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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29
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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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78
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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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40
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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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10
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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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67
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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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1705
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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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48
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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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102
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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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66
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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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23
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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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1393
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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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174
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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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57
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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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Calcium ions displaced from protein complex during the pdb2gmx step
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1
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37
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November 21, 2024
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Gromacs error adding a number 1 to an atom
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8
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112
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October 29, 2024
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Multimer simulation
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1
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49
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October 20, 2024
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Error in the coordinate file sol.gro and topol.gro
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1
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64
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October 19, 2024
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