How can I do a Molecular Dynamics evaluation in protein-ligand approach when I Have A protein with Ca ions?

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Suraj Chougula

Can you suggest a way in which I can generate topology files for protein with GDP in it?

Omid Moradi

thanks for your answer.

this is the main and exact problem.

I have used this code :"gmx pdb2gmx -f REC.pdb -ignh",after that I selected 8 :CHARMM27 forcefield and after that I selected the first option

Thank you for your response

I am still getting fatal error MG301--GDP302 do not have consistent type.

Arpit Jain

Prepare your structure: Include protein, ligand, and Ca ions with proper coordinates.

Select a compatible force field: Ensure it has parameters for Ca ions.

Generate topology: Use gmx pdb2gmx for the protein and modify the topology if needed.

Set up the simulation box: Solvate, add counterions, and perform energy minimization, equilibration, and production MD.

All of which can we easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.