Calcium ions displaced from protein complex during the pdb2gmx step

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1

GROMACS version: 2020

Hello everyone,
I am working with a protein-protein complex in which one of the proteins interact with 4 Calcium ions. I am using charmm36 forcefield with TIP3 water model for the simulation. The complex made of the 2 interacting protein and cal2+ ions was prepared using Alphafold 3 server. However, during the pdb2gmx step, the calcium ions are displaced from their positions and their interactions with the protein are lost (shown in the figure). I have tried to restrain the position of the cal2+ ions with that of
topol.top (1.2 KB)
the proteins but it is not working. Please help me out.

The my_topol.top file is attached for your reference.

In the image below, the PDB model is shown in red, the calcium ions are colored green. The complex.gro file formed after pdb2gmx is shown in blue and superimposed with the PDB structure. The calcium ions are shown in purple.

image
image556×337 70.6 KB

my_topol.top (1.5 KB)

2

You have to make sure you are setting up the correct protonation states of the residues which are in coordination with the Calcium ions. Then you dont even need to restrain it.