Scripts


On this page you will find scripts I have written that I am making available free of charge for anyone to use under the GNU General Public License. Hopefully you will find them useful. While they have been tested to some extent in our laboratory, they may not yet be perfect. Please feel free to contact me if you have any problems, but I do not promise any technical support. By using any of these scripts, you agree to the following terms:

This software is provided as is. I (Justin Lemkul) make no warranty or representation, either expressed or implied, with respect to the software, including its quality, performance, merchantability, or fitness for any particular purpose. The entire risk as to the quality and performance of the software lies with anyone who downloads or uses the software. In no event will I be liable for any damages whatsoever including but not restricted to lost data, revenue, or profits or other direct, indirect, special, incidental, cover, or consequential damages arising out of the use of or inability to use the software, even if advised of the possibility of such damages, except to the extent invariable law, if any, provides otherwise.

Due to server security issues, all scripts are distributed as .txt files. Their names are given as .sh or .pl, depending on the file type, so you can rename the downloaded files if you desire. Just right-click to download any of these scripts.

Most of these scripts are designed to be directly compatible with GROMACS output files or generic single-column data files, but most can be easily extended to deal with other file types. Help and usage information are contained in the header of each file, so please use your favorite text editor to read how to use the scripts properly. If the required input is not provided, the script will die and attempt to teach you how to use it.


Bash shell scripts

trajectory_converter.sh - This shell script converts an mdcrd file generated by AMBER to a GROMACS-compatible .xtc trajectory. The script utilizes functions present within these software packages, so a working installation of both is required for this script to function. The current version of the script allows you to convert a trajectory that contains a protein, water, and up to four types of ions. More ion types could be easily implemented based on the code structure, but we have never had a need for more than two ion types, so four was chosen as an arbitrary stopping point.


Perl scripts

Data Analysis

average_multi.pl - Produces averages and standard deviations of identical data sets from, e.g. replicate simulations.

find_max.pl - Find the maximum of a data set.

find_min.pl - Find the minimum of a data set.

plot_hbmap.pl - Produces a data file that indicates the percentage of time that a given hydrogen bond existed during the trajectory, based on input .pdb, .ndx, and .xpm files.

plot_ss_xpm.pl - Plot the probability of secondary structures by residue number, based on an .xpm file produce by do_dssp.

sham.pl - Creates a suitable input file for g_sham from two input data files.

Membrane Construction and Analysis

area.pl - Calculate the area per lipid for a pure membrane system, based on input box vectors.

bilayer_separator.pl - Produces an .ndx file of the chosen reference atoms in the top and bottom leaflets of a lipid membrane. This is particularly useful for distance measurements or density calculations.

water_deletor.pl - Deletes water molecules that are within the hydrophobic core of a membrane.




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