[gmx-users] struggles with cyclic peptides

[Mark Abraham]

Hi,

Please don't use a digest if you plan to reply to emails, and if you do,
please write a new email with a descriptive subject. Or busy people might
just not bother to find out what your problem is. :-)

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...

Mark

*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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>