Set up multimers: dimers and homodimers

Instructions

Creating a dimer

To create a dimer we first might want to create a template molecule in which we then can set parameters related to the residues protonation, linking and stereochemical state.

Important note: These parameter settings can not be modified after the molecule template has been translated into a molecule in a Molecular System: Once a molecule has been added to a Molecular System, the molecule becomes locked and properties can no longer be modified

To create a dimer, use M: Molecule: Molecules and enter the sequence of the first polymer in the {Add Sequence} tab. Set “Destination Mol System:” to "<None>" to create a molecule template, for which you can define molecular properties. If you want to add the sequence directly to a Molecular System, choose "<New>". Click [Add Sequence!] to create a new molecule/molecule template with the entered sequence.

Now follow the same steps for the second polymer sequence in the dimer. Add this sequence to a new destination molecule and to a new chain but to the same molecular system. Your data should now look something like this in {Chains}:

After the molecule templates have been created, we can use them to create chains and molecular systems. To do this go to {Chains}, select the molecule template in “Template for new chain:” and click [Make Chain From Template].

The same procedure can be used to add additional molecules to the same molecular system to create different kind of multimers

Creating a homodimer

A homodimer can be created either by following the above procedure, or using the following simpler procedure:

• • Create one polymer in the {Add Sequence} tab.

  • Add the polymer to a molecular system by setting the “Destination Mol System:” to "<New>".

  • Go to the {Chains} tab and duplicate the molecule by selecting it and clicking [Copy Chain]. Make sure that the chains in the homodimer have the same |Molecule Template|, the same |Mol System|, but different |Chain Code|: