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    SAMSON Extensions
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    • J
      Jessica last edited by

      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.

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      • Admin
        Admin last edited by

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

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        • J
          Jessica last edited by Jessica 

                         :-) GROMACS - gmx pdb2gmx, VERSION 5.1 (-:

                        GROMACS is written by:
 Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar

          Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
          Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen
          Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner
          Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
          Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
          Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
          Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
          and the project leaders:
          Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

          Copyright (c) 1991-2000, University of Groningen, The Netherlands.
          Copyright (c) 2001-2015, The GROMACS development team at
          Uppsala University, Stockholm University and
          the Royal Institute of Technology, Sweden.
          check out http://www.gromacs.org for more information.

          GROMACS is free software; you can redistribute it and/or modify it
          under the terms of the GNU Lesser General Public License
          as published by the Free Software Foundation; either version 2.1
          of the License, or (at your option) any later version.

          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
          Atomtype 8
          Atomtype 9
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          Atomtype 11
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          Atomtype 32
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          Atomtype 34
          Atomtype 35
          Atomtype 36
          Atomtype 37
          Atomtype 38
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          Atomtype 40
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          Atomtype 42
          Atomtype 43
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          Atomtype 46
          Atomtype 47
          Atomtype 48
          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
          Residue 11
          Residue 12
          Residue 13
          Residue 14
          Residue 15
          Residue 16
          Residue 17
          Residue 18
          Residue 19
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          Residue 25
          Residue 26
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          Residue 31
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          Residue 35
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          Residue 37
          Residue 38
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          Residue 40
          Residue 41
          Residue 42
          Residue 43
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          Residue 46
          Residue 47
          Residue 48
          Residue 49
          Residue 50
          Residue 51
          Residue 52
          Residue 53
          Residue 54
          Residue 55
          Residue 56
          Residue 57
          Residue 58
          Residue 59
          Residue 60
          Residue 61
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          Residue 63
          Residue 64
          Residue 65
          Residue 66
          Residue 67
          Residue 68
          Residue 69
          Residue 70
          Residue 71
          Residue 72
          Residue 73
          Residue 74
          Residue 75
          Residue 76
          Residue 77
          Residue 78
          Residue 79
          Residue 80
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          Residue 82
          Residue 83
          Residue 84
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          Residue 89
          Residue 90
          Residue 91
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          Residue 93
          Residue 94
          Residue 95
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          Residue 99
          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-

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          • Admin
            Admin last edited by

            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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