VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Sat May 26 2018 - 13:44:20 CDT

Ok, so I ran my first ABF simulation on Amantadine in the influenza A M2 channel following this tutorial:

http://www.ks.uiuc.edu/Training/Tutorials/namd/ABF/tutorial-abf.pdf

I set amantdine in the region of the His37 complex with the amine group pointing down. The simulation ran for 5 ns and finished without any errors, and output a .pmf file which I graphed in Excel. So everything seemed to work just fine. But, I did follow this tutorial somewhat blindly while trying to learn how ABF calculations in NAMD work, so not entirely sure if what I did was correct, and the graph wasn't exactly what I expected to see. I've attached my ABF .conf file and Distance.in file for reference. Sorry for this long question, but I really want to understand what I'm doing and not just blindly follow tutorial instructions!

1) I set the lowerboundary to 0.0 and the upperboundary to 30.0. I set group1 atoms to all of the carbons on the carbon cage of amantadine and the group2 atoms to the nitrogens on the the Val27 residues at the C-terminus of the channel. The lowerwallconstant and upperwallconstant to 10.0. Do I understand correctly that the center of mass of the carbon cage will be pulled in the direction of the Val27 nitrogens for a total distance of 30.0 angstroms and a force constant of 10 kcal/mol/A^2?

Should I maybe have set the drug a distance away from the protein's center of mass and pulled the drug toward that as a better reaction coordinate?

2) After I did all of this, I came across what looks like an older ABF tutorial:

http://www.ks.uiuc.edu/Training/Tutorials/science/channel/channel-tut.pdf

  In this tutorial it mentions creating four ABF windows for the ammonium ABF calculation, and then combine the output files to create a PMF. However, what I did gave me a PMF without merging anything or creating multiple windows. So, should I have created multiple windows like they did in the channel-tut.pdf to get a PMF? Or is the script I used the way to get a PMF without multiple ABF windows?

Thanks for all the help so far!!

Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602


  • application/octet-stream attachment: ABF.conf