Gromacs error adding a number 1 to an atom
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8
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58
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October 29, 2024
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Multimer simulation
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1
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15
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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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30
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October 19, 2024
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Inserting a modified residue into a protein/DNA chain using pdb2gmx
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31
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1321
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October 16, 2024
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Complex protein ligand Issue
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1
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25
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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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12
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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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23
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September 6, 2024
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Topology files with packmol
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5
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358
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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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13
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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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28
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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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17
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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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4387
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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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36
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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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71
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July 8, 2024
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Atom OP3 in residue DA 1 was not found in rtp entry DA5 with 30 atoms while sorting atoms
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2
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62
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July 5, 2024
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Creating topology for chimeric DNA/RNA strand
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5
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181
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June 29, 2024
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Atom HD1 in residue HIS was not found in rtp entry HSE with 17 atoms while sorting atoms
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2
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103
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June 25, 2024
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Pdb2gmx Segmentation fault
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0
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56
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June 24, 2024
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How to add new residue in the lipids.rtp in charmm27.ff?
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6
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72
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June 20, 2024
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Error while running writing the topology
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2
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413
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June 18, 2024
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Why CA and CB H atoms in aminoacid residues are not included in topology when gromos FF is used?
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2
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57
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June 1, 2024
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Pdb2gmx for standard lipid in CHARMM; residue name causing issue?
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2
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135
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May 19, 2024
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Modelling POPC lipids with gromos54a7.ff
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3
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114
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May 16, 2024
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Pdb2gmx: Fatal error: Atom CA in residue ACE 1 was not found in rtp entry ACE
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4
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269
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May 15, 2024
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Residue 'DOP' not found in residue topology database
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24
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370
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May 11, 2024
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Capping residue ACE not recognised from the rtp file
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15
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4064
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May 8, 2024
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Program: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2 Source file: src/gromacs/gmxpreprocess/resa
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4
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176
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April 30, 2024
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Difference between x2top and LigParGen ff generation (dodecane)
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1
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111
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April 26, 2024
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Problem with pdb2gmx as it says there is no resdiue type XXX
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6
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256
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April 26, 2024
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