This repository contains several scripts used for trajectory analysis with VMD and CHARMM. The scripts were used in the following publication in Nature Communications: Cryo-EM Structure of the Sodium-driven Chloride/Bicarbonate Exchanger SLC4A8 by Weiguang Wang, Kirill Tsirulnikov, Hristina Zhekova, Gulru Kayik, Hanif Muhammad-Khan, Rustam Azimov, Natalia Abuladze, Liyo Kao, Debbie Newman, Sergei Yu. Noskov, Z. Hong Zhou, Alexander Pushkin, Ira Kurtz
VMD scripts:
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pbcwrap_trajectory.tcl: Wraps and aligns a MD trajectory with respect to selected protein atoms. This results in a MD trajectory with the protein in the center of the periodic cell, which can then be used for further analysis with scripts or VMD tools (e.g. VolMap)
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permeation_count_ions_water.tcl: Evaluates the number of water molecules and Cl, CO3, HCO3, and Na ions which can be found in a region of the protein, defined by provided x, y, and z coordinate ranges, in each frame of a MD trajectory.
CHARMM script:
- ion_time_series.inp: Uses the MIND CHARMM function to select the closest anion and Na ions to a defined region of the protein and then outputs the distance between the ions and the protein for each step of the trajectory. The output can be used for generation of time series of the ions in the binding pocket of the protein.
More information on the usage of the scripts is provided as comments in the scripts.