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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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701
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October 26, 2025
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A Custom Water Force Field Implementation
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0
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51
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October 17, 2025
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Modify residues using CHARMM-GUI pdb reader and manipulator
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0
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77
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October 14, 2025
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Using PMX for ΔΔG on a glycosylated Fc (P238D back-mutation; PDB 3WJJ): viable workflows?
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0
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27
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October 12, 2025
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How to simulate a cyclic protein with AMBER99SB ff?
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1
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76
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October 9, 2025
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Tools for creating initial .gro and combining source files
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0
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35
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October 8, 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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105
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October 7, 2025
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Requesting for claud computing system for md production
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2
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46
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October 7, 2025
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mRNA forcefields issue
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0
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49
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October 5, 2025
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Pdb2gmx fails: Residue 'MGP' not found in CHARMM36 force field
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2
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97
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October 5, 2025
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Inaccurate thermostatting when simulating MD water
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1
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112
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October 4, 2025
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x2top for MINFF
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0
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89
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October 2, 2025
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How to set up protein–peptide complex simulation in GROMACS: peptide as ligand or whole complex?
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1
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153
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September 29, 2025
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Amber04 forcefield check in gromacs
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1
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110
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September 23, 2025
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gmx_ffconv: A Fast, User-Friendly Semi-Automated All-Atom Force Field Converter for GROMACS
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0
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184
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September 21, 2025
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How to generate an .itp file for MoSSe
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0
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29
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September 17, 2025
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Issue generating PFBS anion parameters with LigParGen
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1
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71
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September 15, 2025
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SARS-CoV-2 RNA simulation
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0
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39
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September 8, 2025
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Rigid TIP4P energy and force computations
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8
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154
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September 5, 2025
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Assistance Needed: "Atomtype F not found" Error in GROMACS Minimization with TFE Solvent
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1
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66
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September 3, 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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47
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August 28, 2025
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`No default Improper Dih. types` for ACE-PRO-NME peptide with charmm36-jul2022.ff
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6
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245
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August 18, 2025
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Ligand Topology can't generated
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2
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50
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August 7, 2025
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ImportError: cannot import name 'gcd' from 'fractions'
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10
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4864
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August 7, 2025
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Adding [Fe4S4]+2 cluster parameters to charmm36.ff file
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2
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135
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August 5, 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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27
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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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54
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July 21, 2025
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How to add GAFF force field to gromcs?
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4
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3142
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July 18, 2025
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How to create topology file for amorphous silica?
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3
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152
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July 18, 2025
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How to create restrained file for sol
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0
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31
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July 15, 2025
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