I am new to using AMBER. My pdb id of the protein is 2beg. Also, in simulating this protein with a ligand, do I need to remove the hydrogen atoms of the complex and protein before running in tleap ? Ligands must have hydrogen atoms which can be added through avogadro?
Your help would mean a lot.
Aashish Bhatt
I suggest you use Charmm-gui (https://charmm-gui.org/?doc=input). You can use any force field (amber, charmm, etc. ) and you also able to use MD simulation inputs (amber,NAMD,Gromacs, etc. )
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Arpit Jain
Protein: Load in tleap, add hydrogens. Ligand: Add hydrogens via Avogadro or antechamber. Setup: Combine protein/ligand, add water and ions. Simulate: Run minimization, heating, equilibration, production.
All of which can be easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.
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Smita Patir
Aashish Bhatt Thank you so much for your valuable feedback.
Arpit Jain Thank you so much for your valuable answer.
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