I have a 2D nanostructured drug complex. I want to run an MD simulation for the same using GROMACS. I could not create the force field as it shows errors every time. Can anyone help me?
Arpit Jain
Prepare the structure: Use pdb2gmx to generate the initial structure and topology, ensuring the correct force field is chosen (e.g., CHARMM, OPLS). Generate force field for the drug: If the drug is a non-standard molecule, use ACPYPE or Antechamber to generate the ligand's topology. Solvate the system: Use gmx solvate to add solvent molecules (e.g., water) to the complex. Energy minimization: Run energy minimization with gmx mdrun to relax the system. Modify the .mdp file: Adjust simulation parameters (e.g., temperature, pressure, cutoffs) for the system.
To create an input file for GROMACS:
For errors, check if the force field supports your nanostructure or create custom parameters.
all of which can we easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.
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Aiswarya Thekkedath
Arpit Jain My structure is boron nitride nanocage conjugated with drug. I am unable to create pdb file through mdsim360.
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Aiswarya Thekkedath
@ Arpit Jain i cant able to reply to your message. Please follow me back so that i can reply
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