[gmx-users] dangling bond error no matter what pdb file I use

Justin Lemkul jalemkul at vt.edu
Tue Nov 4 22:55:02 CET 2014



On 11/4/14 4:38 PM, Thomas Lipscomb wrote:
> 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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> Aldert van Buuren  Rudi van Drunen    Anton Feenstra     Sebastian Fritsch
> Gerrit Groenhof    Christoph Junghans Peter Kasson       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     Christian Wennberg Maarten Wolf
> and the project leaders:
> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>
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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
> 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 5.0.1
> 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
> -------------------------------------------------------
>

You haven't added caps onto the input protein, you should expect to get this 
error.  In the tutorial, I build ACE and NH2 groups onto the peptide to 
neutralize the termini.  Since you haven't done this type of modification, 
pdb2gmx will die because you have incomplete amides at the ends of the chain.

The "None" terminus instructs pdb2gmx to not build additional H (in the case of 
NH2 or NH3+ termini) or O(H) (for COO- and COOH).  It doesn't make any chemical 
sense to use "None" for non-capped protein chains.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================


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