[gmx-users] Cyclic Peptide Construction using pdb2gmx issue

Sarah McCartan sarah.mccartan at ucdconnect.ie
Thu Jan 26 18:42:31 CET 2017


I am having an issue building CsA cyclic peptide. It is an 11 residue
peptide with 90 atoms.
I am using the GROMOS 43a2 ff with SPC water model.

I have updated the specbond.dat file with the following:

ALA    C    1    DAL    N    1    0.133    ALA    DAL

I have ensured it is 1 chain in the pdb file and gromacs is identifying the
bond between ALA and DAL but I still get the dangling bond error when I
select NONE for both my termini.

Do I need to modify any other files or amend any inputs?

See screen below for output from pdb2gmx:

Command line:
  gmx pdb2gmx -f csa_start.pdb -o csa_proc.gro -p topol.top -water spce
-missing -ter -ff gromos43a2

Force field 'gromos43a2' occurs in 2 places. pdb2gmx is using the one in the
current directory. Use interactive selection (not the -ff option) if
you would prefer a different one.

Using the Gromos43a2 force field in directory ./gromos43a2.ff

Opening force field file ./gromos43a2.ff/aminoacids.r2b
Reading csa_start.pdb...
Read 90 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 11 residues with 90 atoms

  chain  #res #atoms
  1 'X'    11     90

All occupancy fields zero. This is probably not an X-Ray structure
Opening force field file ./gromos43a2.ff/atomtypes.atp
Atomtype 50
Reading residue database... (gromos43a2)
Opening force field file ./gromos43a2.ff/aminoacids.rtp
Residue 96
Sorting it all out...
Opening force field file ./gromos43a2.ff/aminoacids.hdb
Opening force field file ./gromos43a2.ff/aminoacids.n.tdb
Opening force field file ./gromos43a2.ff/aminoacids.c.tdb
Processing chain 1 'X' (90 atoms, 11 residues)
Identified residue DAL1 as a starting terminus.
Identified residue ALA11 as a ending terminus.
10 out of 10 lines of specbond.dat converted successfully
Special Atom Distance matrix:
   ALA11     C89   0.133
Linking DAL-1 N-1 and ALA-11 C-89...
Select start terminus type for DAL-1
 0: NH3+
 1: NH2
 2: None
Start terminus DAL-1: None
Select end terminus type for ALA-11
 0: COO-
 1: COOH
 2: None
End terminus ALA-11: None

Program gmx pdb2gmx, VERSION 5.1.2
Source code file:
line: 1088

Fatal error:
There is a dangling bond at at least one of the terminal ends. Fix your
coordinate file, add a new terminal database entry (.tdb), or select the
proper existing terminal entry.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

If you need any other information please let me know.
Thanks in advance for your help,

Best Regards


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