[AMBER] umbrella protein-protein

From: Fabian Glaser <fabian.glaser.gmail.com>
Date: Wed, 2 Sep 2020 18:02:55 +0300

Dear Amber community,

I am trying to obtain the DG for the dissociation of protein A - protein B complex running US. The umbrella simulation works, and I get energies, everything looks fine, almost… The difficulty I found is that during the pulling simulation, one of the molecules, in my case the larger one, is being distorted, it seems that part of the area being exposed during the pulling, does not like to be solvated, and then it keep as much as possible in touch with the other molecule. No matter how I choose the center of mass, or how much force I apply it always happens.

I have tried to apply a gentle restraint force on the large molecule, but then energies go to up, and in any case I see this deformation happens.

Is there a way to avoid this fold deformation during the umbrella of this protein-protein complex without restraining too much the system and still getting a good sampling, etc?

Maybe I am thinking wrong, but I imagine that the overall fold should stay stable during the process, correct?

Thanks a lot,



Fabian Glaser PhD

Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/
Tel +972 (0) 4 8293701

AMBER mailing list
Received on Wed Sep 02 2020 - 08:30:02 PDT
Custom Search