Re: Alchemical transformations and DDG of point mutations

From: Jérôme Hénin (
Date: Tue Dec 18 2012 - 07:57:33 CST

Dear Gianluca,

> I wished that the
> mutator
> plugin would leave the original side chain in its position

At this point the side-chains are reconstructed in a default conformation based on internal coordinates. Retaining previous coordinates could be helpful for long side-chains in cases like yours, but it would add some complexity, as the side-chain atoms change names in the process. A part of the code would have to be aware of the mapping between old and new names, and transfer coordinates as needed. If someone is willing to write that code, that's great.


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