[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

[Mark Abraham]

On Wed, Jan 7, 2015 at 3:05 AM, sang eun jee <sangeunjee at gmail.com> wrote:

> 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.
>

Thanks for the comprehensive description.

AMBER force fields generally include only ionic termini and capping groups,
so
that particular expectation isn't reasonable.


> 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
>

I forget whether that is necessary, but it might help.


> to CHYP? But there is no CHYP forcefield is provided in this amber
> forcefield.
>

Welcome to the jungle :-) You could look around at other RES->CRES
differences and decide whether you feel safe parametrizing by analogy, or
you could parametrize CHYP, or you could build on an NME capping group (or
similar).

Mark

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
> -------------------------------------------------------
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