QM/MM Question

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Sun Oct 28 2018 - 21:53:59 CDT

I am setting up a QM/MM simulation with a ligand in an ion channel. I am trying to do this with VMD 1.9.4 alpha's QwikMD. I'd like to select three of the side chains inside of the ion channel and include any waters that

enter these QM regions. I tried selecting the three sidechains and including solvent within 5 angstroms. This tends to select some of the lipids outside of the ion channel as well. How can I keep my QM region to the

ion channel pore, the waters inside, and some of the channel backbone, but exclude the lipids outside of the channel? Thanks!

Kelly L. McGuire

PhD Scholar

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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