[gmx-users] Error: dangling bond at atleast one of terminals

Balasubramanian Suriyanarayanan bsnsuri at gmail.com
Fri May 9 12:25:28 CEST 2014

Dear users,

 I am running membrane protein simulation in lipid environment. when I
processed through pdb2gmx
*pdb2gmx -f 3B5D.pdb -o 3B5D_processed.gro -ignh -ter -water spc*

*I get the following out put and error. *

*please n*

Select the Force Field:
>From '/opt/bio/gromacs/share/gromacs/top':
 1: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
 3: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
 4: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
 5: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006)
 6: AMBER99SB-ILDN force field (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 (with CMAP) - version 2.0
 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: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
15: [DEPRECATED] Encad all-atom force field, using full solvent charges
16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum
17: [DEPRECATED] Gromacs force field (see manual)
18: [DEPRECATED] Gromacs force field with hydrogens for NMR

Using the Gromos53a6 force field in directory gromos53a6.ff

Opening force field file
Reading 3B5D.pdb...
WARNING: all CONECT records are ignored
Analyzing pdb file
Splitting PDB chains based on TER records or changing chain id.
WARNING: Chain identifier 'A' is used in two non-sequential blocks.
They will be treated as separate chains unless you reorder your file.
There are 3 chains and 0 blocks of water and 350 residues with 224 atoms

  chain  #res #atoms
  1 'A'   100    100
  2 'B'    99     99
  3 'A'     1     25

All occupancies are one
Opening force field file
Atomtype 1
Reading residue database... (gromos53a6)
Opening force field file
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing impropers on same bond as a proper
Residue 108
Sorting it all out...
Opening force field file
Opening force field file
Opening force field file

Back Off! I just backed up topol.top to ./#topol.top.4#
Processing chain 1 'A' (100 atoms, 100 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Identified residue TYR6 as a starting terminus.
Identified residue SER105 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for TYR-6
 0: NH3+
 1: NH2
 2: None
Start terminus TYR-6: None
Select end terminus type for SER-105
 0: COO-
 1: COOH
 2: None
End terminus SER-105: None

Program pdb2gmx, VERSION 4.5.4
Source code file: pdb2top.c, line: 1035

F*atal error:*
*There is a dangling bond at at least one of the terminal ends. Select a
proper terminal entry.*
*For more information and tips for troubleshooting, please check the
*website at http://www.gromacs.org/Documentation/Errors


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