[gmx-users] Dihedral between non bonded atoms

Mark Abraham mark.j.abraham at gmail.com
Thu Jul 12 12:19:29 CEST 2018


The list cannot accept attachments, so please find another way to share
your inputs, e.g. a file sharing service. The pdb on its own would not be
enough for anyone to help, because that doesn't tell us what atoms are
concerning you.

By design, pdb2gmx will not try to generate a dihedral if there's no
bond-like interaction in an .rtp building block, so I suspect the issue is
that there is a bond. Distance is not relevant.


On Thu, Jul 12, 2018 at 12:01 PM Momin Ahmad <momin.ahmad at kit.edu> wrote:

> Hi,
> is there a reason why gromacs demands parameters for dihedral angles
> that are not bonded? For example i,j, and k are bonded but l is not. The
> distance of k and l is about 2.7 Angstroem. How can i tell gromacs to
> ignore these dihedrals during pdb2gmx. I did no define a bond in the
> .rtp file. The .pdb i used for pdb2gmx is attached.
> Thanks in advance.
> Cheers,
> Momin
> --
> Momin Ahmad
> Karlsruhe Institute of Technology (KIT)
> Steinbuch Centre for Computing (SCC)
> Hermann-von-Helmholtz-Platz 1
> 76344 Eggenstein-Leopoldshafen
> Phone: +49 721 608-24286 <+49%20721%2060824286>
> E-Mail: Momin.Ahmad at kit.edu
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