Gromacs Wizard Membrane Protein

[Jessica]

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.

[Admin]

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

[Jessica]

               :-) 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
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
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
Residue 20
Residue 21
Residue 22
Residue 23
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Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
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Residue 55
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Residue 58
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Residue 69
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Residue 71
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Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
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Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
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-

[Admin]

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.