Hello Amber Users,
Since last week I have been looking into literature to search for growth of molecules rather than disappearing molecules in AMBER18-TI simulation protocols.
Seems like I could not find anyone in the previous threads who ever posted a query on this...
I was just curious if the developers would guide me on this:
In absolute binding free energy calculations we have timask1=’:C3N’ timask2=’’ ( if we want to annihilate the C3N molecule) but in case we reversed our masks ( timask1=’’ timask2=’:C3N’) would this define my end points to grow a C3N molecule in the kinase pocket?
I am thinking out loud so please correct me if I am thinking it all wrong....
Debarati
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 09 2020 - 16:00:02 PDT
