Gromacs Wizard Membrane Protein



  • Hello,
    I am having difficulty seeing if it is possible to pack lipids into a system containing KALP-15 and DPPC. There is also an error with the Preparation Step (pdb2gmx) where it is trying to build the normal amine and carboxyl groups but I need to add connectivity to the capping groups instead.



  • Hello @Jessica, could you please paste the output of the preparation step in the GROMACS Wizard ?



  •                :-) GROMACS - gmx pdb2gmx, VERSION 5.1 (-:
    
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    GROMACS: gmx pdb2gmx, VERSION 5.1
    Executable: C:\Users\J\AppData\Local\OneAngstrom\SAMSON-Data\0.12.0\Scratch\Elements\02407D21-0490-30BA-D20F-2E88DB100FC5\Resource\gromacs\gmx.exe
    Data prefix: C:\Program Files\Gromacs
    Command line:
    gmx pdb2gmx -f C:/Users/J/AppData/Local/OneAngstrom/SAMSON-Data/0.12.0/Scratch/GROMACS/PDB/temp.pdb -o C:/Users/J/AppData/Local/OneAngstrom/SAMSON-Data/0.12.0/Scratch/GROMACS/GeneratedFiles/KALP-15_PRINC_DPPC128_model.gro -i C:/Users/J/AppData/Local/OneAngstrom/SAMSON-Data/0.12.0/Scratch/GROMACS/GeneratedFiles/KALP-15_PRINC_DPPC128_model.itp -ff gromos53a6_lipid -water spc -p C:/Users/J/AppData/Local/OneAngstrom/SAMSON-Data/0.12.0/Scratch/GROMACS/GeneratedFiles/KALP-15_PRINC_DPPC128_model.top -ignh

    Opening force field file ./gromos53a6_lipid.ff/aminoacids.r2b
    WARNING: all CONECT records are ignored
    All occupancies are one
    Opening force field file ./gromos53a6_lipid.ff/atomtypes.atp

    Atomtype 1
    Atomtype 2
    Atomtype 3
    Atomtype 4
    Atomtype 5
    Atomtype 6
    Atomtype 7
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    Atomtype 47
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    Atomtype 49
    Atomtype 50
    Atomtype 51
    Atomtype 52
    Atomtype 53
    Atomtype 54
    Atomtype 55
    Atomtype 56
    Atomtype 57
    Opening force field file ./gromos53a6_lipid.ff/aminoacids.rtp
    Using default: not generating all possible dihedrals
    Using default: excluding 3 bonded neighbors
    Using default: generating 1,4 H--H interactions
    Using default: removing proper dihedrals found on the same bond as a proper dihedral

    Residue 1
    Residue 2
    Residue 3
    Residue 4
    Residue 5
    Residue 6
    Residue 7
    Residue 8
    Residue 9
    Residue 10
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    Residue 18
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    Residue 100
    Residue 101
    Residue 102
    Residue 103
    Residue 104
    Residue 105
    Residue 106
    Residue 107
    Residue 108
    Sorting it all out...
    Opening force field file ./gromos53a6_lipid.ff/aminoacids.hdb
    Opening force field file ./gromos53a6_lipid.ff/aminoacids.n.tdb
    Opening force field file ./gromos53a6_lipid.ff/aminoacids.c.tdb
    8 out of 8 lines of specbond.dat converted successfully


    Program gmx pdb2gmx, VERSION 5.1
    Source code file: C:\jenkins\workspace\samson-elements\samson-elements\samson-elements-windows\External\gromacs-5.1\src\gromacs\gmxpreprocess\pdb2top.cpp, line: 1127

    Fatal error:
    atom N not found in buiding block 1ACE while combining tdb and rtp
    For more information and tips for troubleshooting, please check the GROMACS
    website at http://www.gromacs.org/Documentation/Errors


    Program: gmx pdb2gmx, VERSION 5.1
    Source file: C:\jenkins\workspace\samson-elements\samson-elements\samson-elements-windows\External\gromacs-5.1\src\gromacs\utility\fatalerror.cpp (line 265)
    Function: void __cdecl do_exit(bool,bool)

    Feature not implemented:
    Fatal error

    For more information and tips for troubleshooting, please check the GROMACS
    website at http://www.gromacs.org/Documentation/Errors

    Using the Gromos53a6_lipid force field in directory ./gromos53a6_lipid.ff

    Reading C:/Users/J/AppData/Local/OneAngstrom/SAMSON-Data/0.12.0/Scratch/GROMACS/PDB/temp.pdb...
    Read 10164 atoms
    Analyzing pdb file
    Splitting chemical chains based on TER records or chain id changing.
    There are 28 chains and 1 blocks of water and 3800 residues with 10164 atoms

    chain #res #atoms
    1 ' ' 17 109
    2 'A' 1 50
    3 'B' 1 50
    4 'C' 1 50
    5 'D' 1 50
    6 'E' 1 50
    7 'F' 1 50
    8 'G' 1 50
    9 'H' 1 50
    10 'I' 1 50
    11 'J' 1 50
    12 'K' 1 50
    13 'L' 1 50
    14 'M' 1 50
    15 'N' 1 50
    16 'O' 1 50
    17 'P' 1 50
    18 'Q' 1 50
    19 'R' 1 50
    20 'S' 1 50
    21 'T' 1 50
    22 'U' 1 50
    23 'V' 1 50
    24 'W' 1 50
    25 'X' 1 50
    26 'Y' 1 50
    27 'Z' 1 50
    28 ' ' 102 5100
    29 ' ' 3655 3655 (only water)

    Reading residue database... (gromos53a6_lipid)
    Processing chain 1 (109 atoms, 17 residues)
    Identified residue ACE1 as a starting terminus.
    Identified residue NH217 as a ending terminus.
    Start terminus ACE-1: NH3+
    End terminus NH2-17: COO-



  • The error message ("atom N not found in buiding block 1ACE while combining tdb and rtp") suggests that, in your model, 1ACE contains a N that should not be there (according to GROMACS topologies). You might have to remove it, or move it to the next residue. You can reorganize atoms, residues, etc. easilyby just dragging nodes around in the Document View.


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