ProteinSwap

[Javier García Marín]

Dear Sire developers,

I am wondering if the module ProteinSwap is available and "ready to use" in the last release of Sire package (and in the windows version?). I have noticed is implemented 

bu I do not know if its works properlty or i it needs still on development. 

Moreover, Is there any way to try to perform WaterSwap calculation using a small peptide segment instead of a ligand parametized with GAFF ? 

Thanks and cheers 

Javier 

[Christopher Woods]

Dear Javier,

Thanks for getting back in touch. I assume everything went well with
your ligandswap and waterswap jobs back in 2018.

ProteinSwap is as ready to use as it can be. It is all implemented,
and the code does work, but we were never able to complete all of the
validation work that would make us confident to publish the method
(and there is no resource now left to complete the work). It looked
hopeful, and gave meaningful results when we tested it on
neuraminidase mutants (e.g. see here
<https://drive.google.com/file/d/0B_KkGMZ8ACfaVFNhVFc2WEFNbzg/view?usp=sharing>).
It is worth playing with, so please feel free to use the program and
see what it does for your systems. Let me know if it works well.

Yes, you can use any ligand you want for any of the "Swap" methods.
However, it will need to be loaded as a ligand, and will be treated as
a ligand. The best way to do this is to setup your system using tleap
etc. as normal, so that you have an amber topology / coordinate file
pair (e.g. rst and top files). Then edit the topology file and rename
the residues in your small peptide so that they are all called "LIG"
(just edit the topology file in a text editor, or I am sure they may
be a way to do this in leap). Then load the file into waterswap etc.
in the same way, saying to use the ligand called "LIG". The peptide
you have renamed will be found, and it should (fingers crossed) work.

Best wishes,

Christopher

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Christopher Woods
+44 (0) 7786 264562
http://chryswoods.com