I want to make MD simulation of a system which ligand (non-standard) covalently bind with protein. Any protocol can be provided? I used to make it as non-covalent binding ligand, but after MD simulation, the covalent bond was broken or disappear.
In a classical MD simulation using standard force fields, you cannot simulate the making or breaking of chemical bonds. However, if you build a protein with a covalently bound ligand, you can subject this to an MD simulation, but you must be able to parameterize the ligand so that it is recognized by the force field you are using.
Yes, you are right. But how can I make force field to recognize ligand and modified residue, especially covalent between ligand and modified residue?
I used to make simulation with Schrodinger. The complex could pass simulation. But after simulation, the covalent bond between ligand and protein disappeared. I tryed to minimized the complex with OPLS field. But the result was same.
Hi Stones,
I think this article will be a great help for you,
http://www.swissparam.ch/SwissParam_gromacs_tutorial.html
Please let me know if you could not.
Thank you very much. It is very useful to make MD simulation of protein and non-covalent binding ligand. I used to try this method, but after simulation, the covalent bond between ligand and protein still disappeared.
which software do you use to simulate? If you use Amber, you can parametrize your non-standard residue by Antechamber. In your case you should consider your ligand and the protein residue which is bound by ligand covalently as a non-standard residue and then try to re-parametrize it.
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