[gmx-users] Cyclic Peptide Construction using pdb2gmx issue

[Mark Abraham]

Hi,

It's been a long time since I tried to do this, but because you are
choosing None then you will probably need to ensure that the hydrogen atoms
are present, and consistent with the cycle.

Mark

On Thu, 26 Jan 2017 18:42 Sarah McCartan <sarah.mccartan at ucdconnect.ie>
wrote:

> Hi,
>
> 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:
>                     DAL1
>                       N1
>    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
> 2
> Start terminus DAL-1: None
> Select end terminus type for ALA-11
>  0: COO-
>  1: COOH
>  2: None
> 2
> End terminus ALA-11: None
>
> -------------------------------------------------------
> Program gmx pdb2gmx, VERSION 5.1.2
> Source code file:
> /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/gmxpreprocess/pdb2top.cpp,
> 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
>
> Sarah
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