[gmx-users] protein ligand complex Energy Minimisation

[Mark Abraham]

Hi,

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.

Mark

Regards
>
> Hershna
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