On Sat, May 11, 2024, Kankana Bhattacharjee via AMBER wrote:
>
>I am trying to understand the tutorial of AMBER Advanced Thermodynamic
>Integration methods to mutate a ligand bound to a protein tutorial.
>Link: https://ambermd.org/tutorials/advanced/tutorial39/index.php
>It is mentioned in the tutorial that, one edge is introduced to convert H
>to Cl i.e, alchemical transformation. But, I would like to know, if I have
>multiple functional groups, then how alchemical change has to be
>incorporated in the TI calculation using ACES ?
The definition of softcore regions determines what alchemical changes are
possible. These need not be restricted to a single functional group.
Note that sampling challenges can become more difficult as the number of
chemical changes increases. Gaining experience by trying out different
transformations can be very helpful. At the beginning, don't worry about
comparing to experiment; your first task should be to convince yourself that
you are getting understandable and reprodicible results.
...good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 14 2024 - 15:00:03 PDT
