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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