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choderalab / mcce-charges

generating ligand charges
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Report May 31 #36

Closed SalahBioPhysics closed 8 years ago

jchodera commented 8 years ago

This is awesome! Thank you!

mrgunner commented 8 years ago

once you get the grant in we can regroup and decide what would be worth doing. Salah will finish up the topology files (this can still be streamlined) We can automate checking the runs and sucking the data out and I would think we could do a few hundred protein ligand complexes easily. It could probably be written up as a stand alone paper.

we would need to see what data is available to support our scan of the protonation effects.

If you need anything else let me know. Good luck with writing & let’s talk when it’s out. m

On Jun 1, 2016, at 2:39 AM, John Chodera notifications@github.com wrote:

This is awesome! Thank you!

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jchodera commented 8 years ago

Sounds good! Revised draft coming shortly.

In the meantime, could you guys raise an issue and list things that we could do to make automation easier? It would be good to capture that information while it is still fresh in your minds.

Let's plan to meet up (virtually or in person) in June to discuss next steps!

jchodera commented 8 years ago

@mrgunner and @SalahBioPhysics: Do you either have some estimate of the statistical error in the computed ligand charges or charge changes, or can you point me to the trajectory output listing the history of protonation states sampled in the run to do a quick statistical analysis? These results are extremely encouraging, but it would be very helpful for me to turn an uncertainty in the change in protons to an uncertainty in free energy error, which could be a significant kcal/mol range that we need to further investigate in follow-up work after the grant is done.

SalahBioPhysics commented 8 years ago

Yes, I re-ran the monte carlo sampling 5 times all at the same ph (ph =7.4). I pushed the changes into github here, you can see that changes in the fort.38 file and sum_crg.out.

I will send you statistical analysis report ASAP.