Covalent MD

Covalent binder to target protein has been attracting great attention in the development of small molecule drugs. VIVA AIDD/CADD platform provide the ability of understanding the dynamics of covalent binder in a protein by the covalent MD simulation module. Here you can upload a prepared covalent complex and start parameterizing your MD simulations!

Upload a prepared protein complex PDB file

Please pick up the covalent bonding atoms

Covalent bonding residues

Force filed for ligand (if present)

gaff

Job name

Job time (hours)

Force filed

AMBER ff14SB

Simulation temperature (K)

Water box

TIP3P
Submit
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