[gmx-users] protein ligand complex Energy Minimisation

Mark Abraham mark.j.abraham at gmail.com
Fri May 5 14:23:34 CEST 2017


On Fri, May 5, 2017 at 1:44 PM Patel, Hershna <h.patel28 at herts.ac.uk> wrote:

> Dear Gromacs users
> I am trying to do energy minimisation of a protein-ligand complex. When
> visualising the output trajectory and .gro file, the structure of the
> ligand becomes distorted. The same thing happens when constraining
> all-bonds during EM. After running grompp, there is this note:   ?
> In moleculetype 'zinc01509994' 12 atoms are not bound by a potential or
>  constraint to any other atom in the same moleculetype. Although
>  technically this might not cause issues in a simulation, this often means
>  that the user forgot to add a bond/potential/constraint or put multiple
>  molecules in the same moleculetype definition by mistake.
> ?Is this causing problems during EM,

Potentially. That's what the message is alerting you to.

> if yes

That's the question for you. Are your non-interacting atoms part of a valid
model of behaviour? Why? Why not? How have other people modelled systems
that are similar to yours?

> then how do I add bonds/potentials/constraints in the same moleculetype?

In the [moleculetype] definition, like all the other interactions in your
overall topolology.

I am using Gromacs version 2016, and generated the ligand .itp/.top/.gro
> files using ACPYPE (the ligand conformation was obtained after docking).

You should a) inspect the resulting topology and conformation for sanity,
and b) be able to simulate your ligand in vacuum without problems. Do that,
as a test of whether you have something that could possibly be used in a
more complex scenario, when docked to a protein.


> Hershna
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