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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