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How can one simulate two ligands? I have a crown ether molecule and another small ligand which is trapped in the crown. Later i plan to study the umbrella sampling for the same.
How can we generate topology files for the above simulation setup?
Any help will be appreciated
In short, you have to manually write the topology. If you already have suitable topologies for both within the framework of an existing force field, it may be as simple as:
If your topologies introduce new atom types or other parameters, those will have to be suitably grouped before any
[moleculetype] can be introduced (see recent threads on exactly this topic).
Thank you for your response. I will try and get back to you in case of any query