[gmx-users] There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files

[sang eun jee]

Hello.
I have an error message from the gromacs system when I used pdb2gmx.
"There is a dangling bond at at least one of the terminal ends and the
force field does not provide terminal entries or files.Fix your terminal
residues so that they match the residue database (.rtp) entries, or provide
terminal database entries (.tdb)."

Simulation structure is collagen, triple helix of (GLY-PRO-HYP)12 built
from TheBuScr program. N-termini is Glycine with N without H and C-termini
is HYP(COO).  TIP3P and AMBER99SB-ILDN protein with F3C Added, nucleic
AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) forcefield
were used.

I expected pdb2gmx add hydrogen atoms to form NH2 and COOH for termini, but
got an error message.

Do I need to edit aminoacids.n.tdp and aminoacids.c.tdp? Or should I change
the name of the Glycine termini in the *.pdb file from GLY to NGLY and HYP
to CHYP? But there is no CHYP forcefield is provided in this amber
forcefield.
I attached full error messages.

Thanks,

==============================================================================================
 /opt/gromacs/4.6.6/bin/./pdb2gmx -f collagen_structure1.pdb -o
processed.gro


Select the Force Field:

 6: AMBER99SB-ILDN protein with F3C Added, nucleic AMBER94 (Lindorff-Larsen
et al., Proteins 78, 1950-58, 2010)

Using the Amber99sb-ildn-f3ca force field in directory
amber99sb-ildn-f3ca.ff

Opening force field file
/opt/gromacs/4.6.6/share/gromacs/top/amber99sb-ildn-f3ca.ff/watermodels.dat

Select the Water Model:
 1: TIP3P     TIP 3-point, recommended

Opening force field file
/opt/gromacs/4.6.6/share/gromacs/top/amber99sb-ildn-f3ca.ff/dna.r2b
Opening force field file
/opt/gromacs/4.6.6/share/gromacs/top/amber99sb-ildn-f3ca.ff/rna.r2b
Reading collagen_structure1.pdb...
Read 687 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
WARNING: Chain identifier 'X' is used in two non-sequential blocks.
They will be treated as separate chains unless you reorder your file.
WARNING: Chain identifier 'X' is used in two non-sequential blocks.
They will be treated as separate chains unless you reorder your file.
WARNING: Chain identifier 'X' 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 108 residues with 687 atoms

  chain  #res #atoms
  1 'X'    36    229
  2 'X'    36    229
  3 'X'    36    229

All occupancies are one
Opening force field file
/opt/gromacs/4.6.6/share/gromacs/top/amber99sb-ildn-f3ca.ff/atomtypes.atp
Atomtype 1
Reading residue database... (amber99sb-ildn-f3ca)
Opening force field file
/opt/gromacs/4.6.6/share/gromacs/top/amber99sb-ildn-f3ca.ff/aminoacids.rtp
Residue 91
Sorting it all out...
Opening force field file
/opt/gromacs/4.6.6/share/gromacs/top/amber99sb-ildn-f3ca.ff/dna.rtp
Residue 107
Sorting it all out...
Opening force field file
/opt/gromacs/4.6.6/share/gromacs/top/amber99sb-ildn-f3ca.ff/rna.rtp
Residue 123
Sorting it all out...
Opening force field file
/opt/gromacs/4.6.6/share/gromacs/top/amber99sb-ildn-f3ca.ff/dna.hdb
Opening force field file
/opt/gromacs/4.6.6/share/gromacs/top/amber99sb-ildn-f3ca.ff/rna.hdb
Opening force field file
/opt/gromacs/4.6.6/share/gromacs/top/amber99sb-ildn-f3ca.ff/aminoacids.n.tdb

Back Off! I just backed up topol.top to ./#topol.top.5#
Processing chain 1 'X' (229 atoms, 36 residues)
Identified residue GLY1 as a starting terminus.
Identified residue HYP36 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully

-------------------------------------------------------
Program pdb2gmx, VERSION 4.6.6
Source code file:
/home/cnbt_01/gromacs_sources/gromacs-4.6.6/src/kernel/pdb2top.c, line: 1104

Fatal error:
There is a dangling bond at at least one of the terminal ends and the force
field does not provide terminal entries or files. Fix your terminal
residues so that they match the residue database (.rtp) entries, or provide
terminal database entries (.tdb).
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------