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2020-08-31 BLFoley

Overview

This repo accompanies a publication detailing an experimental and computational analysis of some mucin-relevant compounds. It contains all the information needed to recreate the simulations, treat the simulated data, and analyze the data. I couldn't include the simulation output or the data from all the treatments and analyses because the file sizes are too large.

Before making the repo, I tried to cull out files that are obviously not relevant. But, this is a large project spanning many years, so here there may be cruft.

Currently, this entire repo, in context with the simulation data, can be accessed at the location below. It's 110+ GB in total.

http://glycam.org/files/2020/Mucin-Like-alpha-Dystroglycan/

Please open a ticket or contact me otherwise if you are having trouble understanding anything in this repo or in the full dataset at the link above.

Contents

parms : The force field parameters that were used to generate the raw data.

RAW : Information relevant to the generation of the raw data.

README.md : This file

scripts : The most recent set of scripts. These are the main scripts used throughout the data generation and analysis. But, see more about this below.

TREATED : Information relevant to any treatments or analyses of the data. See more about this below.

General Notes

Absolute Paths and Other Names

The information contained in the directory called RAW used to live in a path that ended with DLIVE_MD_FINAL_STATE. The data contained in the directory called TREATED used to live in a path that ended with DLIVE. If you see references to these paths, translate accordingly.

As soon as the script forms began to settle, I moved them to my Dropbox. You will probably find path references there. Whenever you see a reference to Dropbox/something/scripts, translate that into the scripts directory.

In both the RAW and TREATED directories, the following definitions apply:

d4g : The short name applied to the GalNAc-modified peptide.

d4m : The short name applied to the Mannose-modified peptide.

protein : The short name applied to the unmodified peptide.

Names such as Eliot, Tolkien, Rime, Nemhain, Hoar, etc., are names of specific computers that were used to perform one or more tasks.

Scripts

The scripts directory at the top level contains the scripts that were used for the majority of the generation and analyses. However, early versions of the scripts might prove to be useful, so they are retained in RAW and TREATED directories as scripts.early and scripts.legacy, respectively.

As an example of a change, consider these older scripts:

RAW/scripts.early/make_cpptraj_files.bash
RAW/scripts.early/make_cpptraj_files_d4m.bash

These two files are nearly identical except that the first is for d4g and the second does some extra work relevant to d4m. They are both named pretty badly because a 'cpptraj file' could mean nearly anything.

They are retained because they were, indeed used. However, in the newer scripts directory, they became this file:

scripts/make_cpptraj_files_for_analysis.bash

...which, in turn, came to have a much nicer name and finally contained code that could be more generally applied:

scripts/make_cpptraj_files_for_NMR_structures.bash

I suspect it will not be difficult to follow trails such as these if needed. But, feel free to contact me if you can't figure something out.

Moved For Safety

Directories called moved_for_safety contain scripts that used to exist at the same level of the directory. But, as the name implies, they were moved for reasons of safety. Specifically, these are scripts designed to be used to start or restart the set of simulations. As such, if run at any time after this initial phase, they could be destructive. They were moved into these directories to minimize the chance that they might be run accidentally.

Most other scripts can be run at any time. They might overwrite existing files, but the new files would be identical (except time stamps and such) or would only update to reflect the current state of the data.

However, don't trust me on the latter. Check first. :-)

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