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

Wang, Yang Yang.Wang10 at utdallas.edu
Fri Jun 1 16:32:44 CEST 2018


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
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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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