Dear Amber experts,
I have a small organic molecule that is covalently bound to two CYS through two C-S bonds. I want to parameterize the small molecule together with the two CYS as a non-standard residue. When preparing the “mc” (main chain) file (see for example section 3 at
https://ambermd.org/tutorials/basic/tutorial5/index.php), I have two sets of Head and Tail names from the two CYS. How to incorporate this information into this “mc” file? Or, is there a better way to do this? Thanks!
Best,
Peng
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Received on Wed Aug 07 2024 - 09:30:01 PDT
