1) No - but the “isolde restrain distances” command also works on nucleic acids, and does accept templates. Should give you essentially the same effect, plus some extra reinforcement of local geometry.
2) Not really - and I’m aware this is a deficiency. In general metal ions don’t behave all that well in classical MD - the parameterisation simply isn’t rich enough to capture their intricacies. I’d love to find a better solution (and to find the time to implement it), but right now the best that’s really possible is to manually add distance restraints between the metal and surrounding atoms. You can add and adjust these using the “simple distance restraints” widget. For these I’d suggest increasing the spring constant quite a bit (try 250 or 500).
— Tristan
Good Morning. I have two more quick questions about using Isolde:
1) Can another model be used as a template for the 'isolde restrain basepairs' command?
2) is there a way to set restraints to coordinate the waters around a Mg ion, for example (i.e. so they have the correct geometry)?
I'm afraid not. MD parameters are more difficult to transfer to the traditional crystallographic restraint schemes than you might first think. You'll need to use one of the dedicated restraint generation tools like phenix.elbow or CCP4's AceDRG. Using eLBOW, for more complicated ligands I've generally gotten best results in the past by using its optional plugin to ORCA (
https://www.faccts.de/docs/orca/5.0/tutorials/).
-- Tritan
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