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Segmentation fault in MARTINI 2.2 with pulling
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16
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40
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February 12, 2025
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ACPYPE Error: Exceeded Max Bond Limit (512) – How can I fix this?
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0
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14
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February 12, 2025
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Fatal error: -ter not working, atom C1 not found
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0
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15
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February 10, 2025
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Is it possible to use different forcefields for protein and ligand when running MD simulation?
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0
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9
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February 10, 2025
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Adding a new residue covalently linked to multiple cysteines
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0
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26
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February 6, 2025
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Understanding .hdb format
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2
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25
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February 6, 2025
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H-bond constraint
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4
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2032
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February 6, 2025
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Question about modification of forcefield for non-standard residues
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0
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15
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February 5, 2025
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How to simulate d-amino acids
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9
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112
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February 4, 2025
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Membrane Protein ligand simulation
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7
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66
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February 3, 2025
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CHARMM force field parameters for Ru(II)
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0
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32
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January 29, 2025
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Residue 'FE' not found in residue topology database
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0
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17
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January 29, 2025
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Resolving Charge Imbalance for CHARMM DNA Backbone Parameterization in GROMACS
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2
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19
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January 28, 2025
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Zero OPLS Lennard-Jones parameters for H atoms and overlapping atoms
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5
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799
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January 24, 2025
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Protonation States in the OPLS-AA Forcefield
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0
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11
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January 24, 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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14
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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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21
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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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7
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January 22, 2025
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DNA Backbone Parametrization and rtp File
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1
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35
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January 20, 2025
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NPT Step Issue with Protein 1QS4 (4 Waters and Mg²⁺ in Active Site)
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4
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28
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January 22, 2025
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How to use the charmm36 force field parameters from CGenFF for ligand?
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1
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101
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January 21, 2025
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Issue with pdb2gmx when peptide is capped
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4
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32
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January 21, 2025
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Questions About CHARMM36 Parameters for DNA Systems
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2
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36
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January 17, 2025
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Help, adding PEG to my gro and top file-is not placed where it should be
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4
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33
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January 17, 2025
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Chloroform as a solvent in Charmm36 force field
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1
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38
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January 16, 2025
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Estimated Oscillation Time period less than timestep
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4
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32
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January 15, 2025
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Does anyone have validated GAFF parameters for the PEG400?
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0
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6
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January 13, 2025
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Adding an organic molecule to OPLS-AA force field
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0
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34
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January 11, 2025
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Ion Parameters in Amber99bsc1 Force Field
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0
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8
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January 10, 2025
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On FF parameterization of molecules with non-zero valence
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3
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11
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January 10, 2025
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