Should I solvate and/or add counter ions?

This question references the Options available when using the Glycoprotein Builder or any of the various interfaces to the Carbohydrate Builder (e.g., GAG Builder, Build-by-URL, Interactive Builder).

In general, if you do not know for certain that you need to solvate or add counter ions, then you do not need to.  These options are typically only useful if you are planning to run a simulation of the system’s behavior in solvent.  If you only need a reasonable representation of the molecular structure, then you probably do not need either.  In some very highly charged systems, the use of counter ions might be advisable, but, again, if you are not running a simulation, you do not need to solvate.

Note that the option to add counter ions will only be visible if your system has a non-zero net charge.

Here are images showing the step in the build process where the Options dialog is visible:

Carbohydrate Builder:

Glycoprotein Builder:

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