Hello!
I am wondering if there is a GUI interface or a more automated way to build the protein-ligand or protein-DNA MD system that will go through various steps starting from PDB structure, clean up/add missing loops/disulfide formation, solvation, neutralization of the system, adding salt, and generate relevant complex topology files (e.g., some Knime workflow).
If not, can a solvated protein-ligand/protein-DNA system from Maestro be used to generate the input topology and coordinate files using LeaP program for running Amber simulations?
Best regards,
Jhuma
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Received on Mon Nov 01 2021 - 13:00:02 PDT
