yes, there is a way to set the “pH” of the system, but is not available from the pre-configured workflows. You will need to prepare your own workflow step by step. The operation you are looking for is named “Set ionization state” and is available from a topology input. For example you can first run a “Generate topology for Amber” operation from your input PDB, and then run the “Set ionization state” modifying the input pH of the system (see attached image). You can also choose from two different methods here: propka (approximate) or CMIP (rigorous). Same happens with the salt concentration, which can be modified when solvating with the operation named “Solvate structure” (see image).
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In BioExcel we are trying to update this idea of free MD services (at least setup + configuration files) through GUIs such as web servers. Stay tuned with BioExcel web page or subscribe to our mailing list to hear about the news!