[gmx-users] Doubts about molecular dynamics of a protein with one ZN binding site

[Sebas Ayala]

Hello Gromacs community,

I am performing a molecular dynamics simulation from CRBN protein (PDB ID:
4tz4), which contain a ZN binding site composed of four cysteines. The main
goal is understanding the chemical and biological changes in the Zn binding
site from this protein when Cys391-to-Arg (C391R) substitution occur. For
this, we performed the geometry optimization of the complex of four
cysteines and Zn using DFT calculations on Gaussian 16 suite. Then, we put
the coordinates obtained through DFT on the PDB format, and we will perform
molecular dynamics simulation to obtain results in the perspective of the
whole protein.

Now, I am using Gromacs to perform the MD simulation, but there is an error
on my simulation during the NVT stabilization. This is the error message:

"Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1#
Wrote pdb files with previous and current coordinates
^Mstep 0
WARNING: Listed nonbonded interaction between particles 4204 and 4221
at distance 4.402 which is larger than the table limit 2.029 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason."

I am thinking about the reason for this error, and this could be because
the force field which I am using to perform the simulation (amber03), but I
am not sure about that. It is proper to mention that the atoms in which
there is the error are the C of the residues (Lys324 and Gly325) which are
between two of the Cys that form the Zn binding site.

Please, can you help me with this issue?

Best regards

Sebastian Ayala