[gmx-users] dangling bond error no matter what pdb file I use
Thomas Lipscomb
linuxborg2 at yahoo.com
Tue Nov 4 22:41:16 CET 2014
Dear Gromacs mailing list,
I am at this step in a protein in membrane tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html
cd /home/tlipscomb/Desktop/Antimicrobial_Peptides/Gromacs/KALP
/usr/local/gromacs/bin/gmx pdb2gmx -f 1SG0.pdb -o 1SG0_processed.gro -ignh -ter -water spc
13
2
2
13 is GROMOS96 53A6
2 means no terminus type
I get this error, please help:
-------------------------------------------------------
Program gmx, VERSION 5.0.1
Source code file: /home/tlipscomb/gromacs-5.0.1/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1091
Fatal error:
There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
I know that 1SG0.pdb is correct because it worked for me on DOCK6 and it came from the PDB database. Is it the .tdb file messing up Gromacs? I just installed Gromacs and I thought that the .tdb file it came with is fine.
This is what I have done so far with Gromacs:
Installed Gromacs on linux
cd /home/tlipscomb/Desktop/Antimicrobial_Peptides/Gromacs/KALP
/usr/local/gromacs/bin/gmx pdb2gmx -f 1SG0.pdb -o 1SG0_processed.gro -ignh -ter -water spc
13
2
2
That's it.
Once we resolve this bug I will go back to using model1.pdb (Maximin 3 peptide alpha helix) because that is the protein I need to simulate interacting with the membrane.
This is the full command line stuff that happened:
[tlipscomb at prime-radiant KALP]$ /usr/local/gromacs/bin/gmx pdb2gmx -f 1SG0.pdb -o 1SG0_processed.gro -ignh -ter -water spc
GROMACS: gmx pdb2gmx, VERSION 5.0.1
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Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
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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 Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
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Copyright (c) 2001-2014, The GROMACS development team at
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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
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GROMACS: gmx pdb2gmx, VERSION 5.0.1
Executable: /usr/local/gromacs/bin/gmx
Library dir: /usr/local/gromacs/share/gromacs/top
Command line:
gmx pdb2gmx -f 1SG0.pdb -o 1SG0_processed.gro -ignh -ter -water spc
Select the Force Field:
>From '/usr/local/gromacs/share/gromacs/top':
1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
14
Using the Gromos53a6 force field in directory gromos53a6.ff
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b
Reading 1SG0.pdb...
WARNING: all CONECT records are ignored
Read 'NRH DEHYDROGENASE [QUINONE] 2; 5 OXIDOREDUCTASE 2', 4143 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
WARNING: Chain identifier 'A' is used in two non-sequential blocks.
They will be treated as separate chains unless you reorder your file.
WARNING: Chain identifier 'B' is used in two non-sequential blocks.
They will be treated as separate chains unless you reorder your file.
Moved all the water blocks to the end
There are 4 chains and 2 blocks of water and 819 residues with 4143 atoms
chain #res #atoms
1 'A' 230 1824
2 'B' 230 1824
3 'A' 3 71
4 'B' 3 71
5 ' ' 163 163 (only water)
6 ' ' 190 190 (only water)
All occupancies are one
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/atomtypes.atp
Atomtype 57
Reading residue database... (gromos53a6)
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.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 108
Sorting it all out...
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.hdb
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb
Processing chain 1 'A' (1824 atoms, 230 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 341 donors and 337 acceptors were found.
There are 501 hydrogen bonds
Will use HISE for residue 11
Will use HISE for residue 72
Will use HISE for residue 173
Will use HISE for residue 177
Will use HISE for residue 225
Will use HISD for residue 227
Identified residue ALA1 as a starting terminus.
Identified residue GLN230 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
HIS11 CYS34 MET44 HIS72 MET116 CYS121 MET154
NE284 SG258 SD332 NE2555 SD923 SG964 SD1202
CYS34 SG258 2.498
MET44 SD332 1.591 2.048
HIS72 NE2555 3.570 3.204 2.500
MET116 SD923 1.685 2.297 1.437 1.990
CYS121 SG964 2.870 2.709 1.741 0.763 1.418
MET154 SD1202 1.814 3.506 3.172 4.279 2.374 3.784
HIS173 NE21365 2.911 2.892 2.826 2.078 1.469 2.023 2.749
HIS177 NE21394 3.003 2.433 2.736 2.005 1.588 1.954 3.060
CYS179 SG1411 2.552 2.310 1.895 1.273 0.924 0.956 3.121
MET203 SD1594 1.374 2.364 2.587 4.111 2.207 3.533 1.368
CYS222 SG1753 2.564 2.364 2.567 2.311 1.318 2.104 2.499
HIS225 NE21775 3.457 3.333 3.854 3.483 2.568 3.414 2.628
HIS227 NE21799 2.352 2.525 2.625 2.635 1.327 2.365 2.069
HIS173 HIS177 CYS179 MET203 CYS222 HIS225
NE21365 NE21394 SG1411 SD1594 SG1753 NE21775
HIS177 NE21394 0.655
CYS179 SG1411 1.152 1.046
MET203 SD1594 2.820 2.833 2.874
CYS222 SG1753 0.608 0.563 1.150 2.330
HIS225 NE21775 1.451 1.578 2.475 2.755 1.365
HIS227 NE21799 0.809 1.002 1.444 2.040 0.450 1.252
Select start terminus type for ALA-1
0: NH3+
1: NH2
2: None
2
Start terminus ALA-1: None
Select end terminus type for GLN-230
0: COO-
1: COOH
2: None
2
End terminus GLN-230: None
-------------------------------------------------------
Program gmx, VERSION 5.0.1
Source code file: /home/tlipscomb/gromacs-5.0.1/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1091
Fatal error:
There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Sincerely,
Thomas
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