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What parameters should be changed in mdp file to use wth CHARMM force field?
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3
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41
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March 29, 2023
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How to do the PTM (post-translational modification) using OPLS-AA forcefield?
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0
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15
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March 24, 2023
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Mis match bwtween the topol.top and solv.gro file
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13
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69
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March 19, 2023
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Difference between bond function type 1 and 6
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1
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22
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March 17, 2023
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Generate topolgy file using pdb and itp files
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2
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71
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March 16, 2023
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How to find out the topology parameter file of a molecule suitable for CHARMM force field using ATB
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1
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62
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March 16, 2023
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Fatal errors in .rtp file
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2
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46
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March 16, 2023
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Newest CHARMM36 port for GROMACS
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13
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4229
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March 16, 2023
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Forcefield to simulate RNA molecules containing modifications with GROMACS and amber ff
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0
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27
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March 16, 2023
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Segmentation fault when gmx pdb2gmx
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3
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34
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March 16, 2023
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How to build 2Fe-2S cluster model for simulation?
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4
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35
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March 16, 2023
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WARNING: Duplicate line found in or between hackblock and rtp entries using AMBER99sb-ildn
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3
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55
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March 13, 2023
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ImportError: cannot import name 'gcd' from 'fractions'
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2
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124
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March 6, 2023
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Parrinelo-rahman parameters and thermostat for lipid membranes using charmm C36m
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2
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47
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March 3, 2023
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Cmap potentials in GROMACS 2019 and after
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9
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91
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March 3, 2023
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Can you please suggest a forcefield that can be used to simulate the gold nano particle interactions
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1
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35
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March 3, 2023
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Error message
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2
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39
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February 26, 2023
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Atom type of hydrogen of SPCE water model in charmm36 force field?
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1
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40
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February 25, 2023
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Virtual sites in residues
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0
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28
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February 24, 2023
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Paramatrization of Hydrogen Sulfide
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0
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21
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February 24, 2023
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Using amberff14SB + parmbsc1
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0
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27
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February 24, 2023
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Can amber14sb-parmbsc1 force field file be used for protein simulation?
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2
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210
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February 24, 2023
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CHARMM force field parameters for metal ions Cd(II) and Pb(II)
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1
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38
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February 22, 2023
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An error while executing command : gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
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5
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512
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February 17, 2023
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Amber prep & frcmod files to gromacs
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3
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59
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February 16, 2023
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Simulation Breaks the system (separates both the chains of the Antibody)
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9
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83
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February 16, 2023
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CHARMM36 Non-natural amino acid NAL parameter when it is in N and C terminals?
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4
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74
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February 11, 2023
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Unknown cmap torsion
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4
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54
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February 10, 2023
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Can't create topology for small molecule using pdb2gmx/x2top
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1
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49
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February 10, 2023
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Grompp error
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8
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76
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February 7, 2023
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