How to simulate two ligands? My setup doesnt include any polypeptide

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1

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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

2

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:

#include "parent.ff/forcefield.itp"
#include "crown_ether.itp"
#include "ligand.itp"
[system]
my system
[molecules]
crown_ether 1
ligand 1

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).

3

Thank you for your response. I will try and get back to you in case of any query