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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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7
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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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5
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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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5
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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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23
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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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1454
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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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20
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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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21
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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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23
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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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15
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December 17, 2024
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How to simulate d-amino acids
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12
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67
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December 10, 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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1005
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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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55
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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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12
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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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35
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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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13
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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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26
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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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67
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October 29, 2024
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Multimer simulation
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1
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24
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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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47
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October 19, 2024
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Complex protein ligand Issue
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1
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35
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October 1, 2024
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Non-standard amino acid alchemical mutation - dihedrals error
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1
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27
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September 25, 2024
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Check the Forcefield of the electrolyte system EC DEC DMC
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1
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21
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September 9, 2024
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Fatal error: Atom N in residue AGLC 0 was not found in rtp entry AGLC with 24 atoms while sorting at
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0
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30
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September 6, 2024
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Topology files with packmol
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5
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405
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September 4, 2024
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Using pdb2gmx as a lib
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0
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15
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August 20, 2024
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Fatal error: Atom OXT in residue VAL 10 was not found in rtp entry VAL with 16 atoms while sorting
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1
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45
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August 6, 2024
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Protein capping using Ace for amber99sb-ildn
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0
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19
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July 31, 2024
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Help on how to solve "atom N not found in building block 1ADE while combining tdb and rtp"
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9
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4496
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July 17, 2024
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Problem with force field parameters for Metallprotein
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0
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51
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July 13, 2024
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Hdb and rtp file generation
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1
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94
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July 8, 2024
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