VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Wed Jul 18 2018 - 20:22:06 CDT

Thanks for the response. I could see it happening during the MD/ABF simulation step because the restraints are off. But the restraints are on during the minimization, annealing, and equilibration steps, and I haven't seen the alpha helices change form until I started adding water to the channel as part of the starting structure. Before, I would delete all waters in the membrane and channel. But lately I've been keeping the water in the channel after solvating the system (still deleting the waters in the membrane). Could this be a problem with not minimizing and equilibrating long enough before going into the ABF simulation? I minimize for 3000 steps and equilibrate for 1 nanosecond.

Kelly L. McGuire

PhD Scholar

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Robin Betz <robin_at_robinbetz.com>
Sent: Wednesday, July 18, 2018 7:14:47 PM
To: McGuire, Kelly
Cc: Vmd l
Subject: Re: vmd-l: New Cartoon and Simulation Question

Hi Kelly,

Secondary structure assignment is done with STRIDE or similar.
You can read how the algorithm functions in the original paper: http://webclu.bio.wzw.tum.de/stride/stride.pdf
Are you recalculating the secondary structure as you go? You can call "ssrecalc <molid>" in the TCL interpreter to do this and the cartoon representation will be updated based on the current frame.

More qualitatively, if you remove the restraints from a protein, it then becomes free to sample more conformations. Some of those conformations may have fewer helical regions than others. Whether or not those conformations are valid or relevant is up to you.

Hope this helps,
Robin

On Wed, Jul 18, 2018 at 6:08 PM McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:

This might be a question for the NAMD mailing list as well. I have a homotetramer ion channel in a lipid bilayer, and each peptide of this channel is completely alpha helical. Sometimes after I minimize, or anneal, or equilibrate, or even at my ABF step of the simulation I'll notice parts of the alpha helices (new cartoon representation) becoming more like the tube representation. During minimization, annealing, and equilibration there is a backbone restraint on the protein (none on the bilayer, water, or ions), and then at the ABF step, all restraints are off. What could be some of the causes for alpha helices in the new cartoon representation to shift toward more tube like representations?

Kelly L. McGuire

PhD Scholar

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602