[gmx-users] specbond

[Mark Abraham]

Hi,

Normally rtp entries specify the bonds and all the angles are inferred and
the parameters for everything are deduced from atom types. That's the same
with bonds that originated from specbonds.dat entries.

Note that if the MOF has head to tail bonding then you can use the same
mechanism as the protein force fields use, with + and - notations (see docs
and the examples in aminoacids.rtp).

Mark

On Wed, Jul 25, 2018, 17:14 Momin Ahmad <momin.ahmad at kit.edu> wrote:

> Hello,
>
> i parametrized two component of my metal-organic framework as modular
> building block. Each component has an entry in the .rtp file and pdb2gmx
> and grompp do work. Now i want to define bonds between both residues. In
> specbond.dat it is possible to do so but where do i put in the new
> force-field parameters for additional bonds, angles, dihedrals that are
> formed by the intermolecular bond?
>
> Kind regards
> 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
> E-Mail: Momin.Ahmad at kit.edu
>
> --
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