Re: ABF Questions

From: McGuire, Kelly (
Date: Sat Jul 21 2018 - 09:52:31 CDT

Thanks for the response! I'm trying to figure out why the free energy profile of my ion channel and ligand has about 50 kcal/mol higher energy with the ligand exiting into bulk water on the C-terminus side vs exiting the N-terminus side into bulk water. They should be about equal energy, right? That doesn't seem correct...

Kelly L. McGuire

PhD Scholar


Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

From: Jrme Hnin <>
Sent: Saturday, July 21, 2018 5:03:39 AM
To: Namd Mailing List; McGuire, Kelly
Subject: Re: namd-l: ABF Questions

On Sat, 21 Jul 2018 at 04:17, McGuire, Kelly <<>> wrote:

Two questions about ABF:

1) Right now I have the center of mass of my ligand as the main atoms and the center of mass of my protein as the ref atoms (i.e. all of the CA C N O atom types of the backbone). But if for my ref atoms I just the center of mass of one of the side chains near the middle of the protein, could this change my PMF results drastically? How critical is the choice of ref atoms within the protein for ABF with a ligand in the protein?

That is actually a question about your protein, not about ABF.

(Is there a limit of atom numbers that can be used for the ref atoms?)

There is no limit. Large numbers will incur a performance penalty, but a few dozens or even a couple hundred should be fine - especially with a center-of-mass-based coordinate.

2) The lowerboundarywall and upperboundarywall are used essentially to keep say a ligand within the specified window, but how much does the choice of value itself have an effect on the PMF result? Would 10 kcal/mol vs 100 kcal/mol for these values have a large effect on my results?

Most likely not. The only case that could be a problem is a PMF that is steeply decreasing towards the boundary, but it is more typically increasing.


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