Alanine scanning with openmm!

The functionality of OpenMM will (eventually) include everything that one would need to run modern molecular simulation.
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Omar Abuyaman
Posts: 31
Joined: Mon Apr 22, 2019 11:12 am

Alanine scanning with openmm!

Post by Omar Abuyaman » Wed Dec 25, 2019 4:13 am

Hi
I wonder if there is a way to do Alanine scaning with openmm as it make a lot of sense here with the very fast openmm, like 10ns MD with each mutation for 200 aa long polypeptide.
Thanks
Omar
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Peter Eastman
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Joined: Thu Aug 09, 2007 1:25 pm

Re: Alanine scanning with openmm!

Post by Peter Eastman » Thu Dec 26, 2019 12:46 pm

It would be pretty easy to do this with PDBFixer (https://github.com/pandegroup/pdbfixer). It has an applyMutations() function that makes this very simple. See https://github.com/pandegroup/pdbfixer/ ... #L729-L761.
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