Hi, I am wondering how did this panel do the alignment when using the first frame as the reference structure? Based on CA, backbone, side chain or...? Thanks!
Hi, very nice video tutorials. Thanks for it. I have following questions: is it possible to do a QM/MM simulation also of a protein-ligand system as easily as demonstrated in these Desmond videos? Also kindly let me know if free energy of binding can be straightway calculated using Desmond.
Hi Sinha Suman, Thanks for your comment. Yes, you can do a QM/MM simulation of protein-ligand systems using Schrödinger's program QSite (www.schrodinger.com/QSite/). We don't currently have any video tutorials for QSite, however, the QSite User Guide contains detailed information including a tutorial. It is available via Maestro or from www.schrodinger.com/supportdocs/ Once opened within Maestro the QSite panel quick help button also contains details on how to set up and use the panel. Best regards, Jarred
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