[AMBER] Growing of small molecules instead of annihilation of molecules in amber TI simulations

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Wed, 9 Sep 2020 22:35:40 +0000

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
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Received on Wed Sep 09 2020 - 16:00:02 PDT
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