Re: Alchemical transformations and DDG of point mutations

From: Gianluca Interlandi (
Date: Tue Dec 18 2012 - 12:53:21 CST

Dear Jérôme,

I think that the mutator does a great job. It's important though that the
user is aware of that. Running psfgen and alchemify manually solves the
problem for me. There, I generally leave the backbone atoms and the Cbeta
of the target side chain in place and let "guesscord" (resp. IC PARA - IC
BUILD in CHARMM) reconstruct the rest.



On Tue, 18 Dec 2012, Jérôme Hénin wrote:

> 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.
> Cheers,
> Jerome

Gianluca Interlandi, PhD
                     +1 (206) 685 4435

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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