Examples for a section of the Molecular Structure Checking wf

BioBB
1

Hi,
in the section Metal Ions of the Molecular Structure Checking wf there is written the following:
“Presence of heteroatoms being metal ions.
Only structural metal ions should be kept in MD simulations, as they require special force field parameters.
In some cases, the atomic coordination between the protein atoms and the metal ions should be also specified.”

It is possible to have code examples relative on how to use biobb in the two mentioned case?

Thanks.

Saverio

2

Hi Saverio,

I’m afraid we don’t have any example for these cases at this stage. But anyway, that depends a lot on the MD engine used. For example, in GROMACS you can coordinate ions manually modifying the specbonds file or the topology files (see for example Using specbond.dat to define Zn-Cys bonds - User discussions - GROMACS forums or Zinc Finger Bonded Method - User discussions - GROMACS forums), which is not possible with BioBB because there’s no GROMACS command available for that which we can wrap (it requires manual modification of files). Instead, in AMBER you can include specific bonds in tleap in combination with forcefield parameters containing the description of the coordinated ion (which could be different than the ion without coordination, e.g. https://doi.org/10.1021/acsomega.0c01337, https://ambermd.org/tutorials/advanced/tutorial20/ZAFF.php).
On the other hand, you could also play with position restraints/constraints, again different depending on the MD engine, available as input parameters in AMBER (restraint_wt +
restraintmask), but also requiring manual modification of topology files in GROMACS (see for example Applying distance constraints to ligand and Mg ion - #5 by joshhayden - User discussions - GROMACS forums).
Hope this helps!

3

Hi Adam,
thanks for the suggestions.

Saverio