Re: ABF Questions

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Fri Jul 20 2018 - 21:20:25 CDT

I meant lowerwallconstant and upperwallconstant for question 2).

Kelly L. McGuire

PhD Scholar

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of McGuire, Kelly <mcg05004_at_byui.edu>
Sent: Friday, July 20, 2018 8:13:43 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: ABF Questions

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

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?

Kelly L. McGuire

PhD Scholar

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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