[gmx-users] Dangling bond error using Amber force field.

Fri Jun 1 17:05:09 CEST 2018

Hi,

Chain 16 is clearly a problem (start and end residue is NME 8) but you'll
have to look at the contents of the pdb file to understand its contents.

Mark

On Fri, Jun 1, 2018, 16:33 Wang, Yang <Yang.Wang10 at utdallas.edu> wrote:

> Hi,
>
> I am dealing with a protein model using Gromacs. I got the PDB file from
> RCSB bank (PID: 2slk) and I modified the residue name according to the rtp
> file. Since the start terminal is ACE, I modified the end terminal from
> GLY/ALA to CGLY/CALA.  I ran it with pdb2gmx command but I still got the
> dangling bond error.  The error message showed that the error came from the
> last chain of NEM residues. I guess it is probably still the name issue for
> the NEM cap. I am wondering what residue name I should use for NEM.
> Thanks a lot!
>
> Command:
> login2.ls5(1076)$ gmx pdb2gmx -f 2slk.pdb -o 2slk_processed.gro -water
> tip3p -ignh
>
> Error:
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Select the Force Field:
> From '/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top':
>  1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
> 1999-2012, 2003)
> ..........( Omit the other force fields)
>
> 1
>
> Using the Amber03 force field in directory
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff
>
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.r2b
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/dna.r2b
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/rna.r2b
> Reading 2slk.pdb...
> WARNING: all CONECT records are ignored
> Read '2 FIBROIN PEPTIDES. I. SHEETS OF POLY(ALA-GLY) CHAINS', 480 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.
> There are 16 chains and 0 blocks of water and 106 residues with 480 atoms
>
>   chain  #res #atoms
>   1 'A'     7     30
>   2 'B'     7     30
>   3 'C'     7     30
>   4 'D'     7     30
>   5 'E'     7     30
>   6 'F'     7     30
>   7 'G'     7     30
>   8 'H'     7     30
>   9 'I'     7     30
>   10 'J'     7     30
>   11 'K'     7     30
>   12 'L'     7     30
>   13 'M'     7     30
>   14 'N'     7     30
>   15 'O'     7     30
>   16 'A'     1     30
>
> All occupancies are one
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/atomtypes.atp
> Atomtype 68
> Reading residue database... (amber03)
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.rtp
> Residue 93
> Sorting it all out...
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/dna.rtp
> Residue 109
> Sorting it all out...
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/rna.rtp
> Residue 125
> Sorting it all out...
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.hdb
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/dna.hdb
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/rna.hdb
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.n.tdb
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.c.tdb
>
> ..........( Omit the chain 1-15)
>
>
> Processing chain 16 'A' (30 atoms, 1 residues)
> Identified residue NME8 as a starting terminus.
> Identified residue NME8 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
>
> -------------------------------------------------------
> Program gmx pdb2gmx, VERSION 5.1.2
> Source code file:
> /admin/rpms/BUILD/gromacs-5.1.2/src/gromacs/gmxpreprocess/pdb2top.cpp,
> line: 1083
>
> 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
> -------------------------------------------------------
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
>
> Best Regards,
>
> Yang Wang
>
>
>
> Ph.D. student
>
> Department of Mechanical Engineering
>
> University of Texas at Dallas
>
> E-mail: yxw152130 at utdallas.edu<mailto:sxw141830 at utdallas.edu>
>
> --
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