[gmx-users] struggles with cyclic peptides

Mark Abraham mark.j.abraham at gmail.com
Sat Sep 12 13:59:18 CEST 2015


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On Sat, Sep 12, 2015 at 7:25 AM Nikhil Maroli <scinikhil at gmail.com> wrote:

> Thanks Mark and Joao
> I'm  able to make peptide bond for the Cyclic peptide using specbond.dat
> but there is a additional Oxygen and Hydrogen atom on the Carbon and
> Nitrogen atom.when i run pdb2gmx selected Amber forcefield  it didnt ask
> for the terminals and created topology with amid bond for the cyclic
> ring.

AMBER handles temini differently from CHARMM.

> but when i select the CHARMM forcefield it asking for the terminals
> and selected NONE but  it shows the error even after done as you said
> before ( Remove the chain ID or make them all chain A.

NONE means "don't add any of the pre-defined sets of terminal atoms" but if
you want a specbond and there are extra atoms present, pdb2gmx can't read
your mind and delete the extra atoms. I don't know if that's the problem,
because unfortunately you haven't shared the pdb2gmx output that would
suggest where the extra bond is found...


*There is a dangling bond at at least one of the terminal ends. Fix
> yourcoordinate
> 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*
> Thanks
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