[NOMAD Laboratory CoE](http://nomad-coe.eu) parser for [CHARMM](https://www.charmm.org/charmm/)
## Version 0.0.2
This is a NOMAD parser for [CHARMM](https://www.charmm.org/charmm/). It will read CHARMM input and
output files and provide all information in NOMAD's unified Metainfo based Archive format.
This is the parser for CHARMM (Chemistry at HARvard Macromolecular Mechanics) code in [CHARMM](https://www.charmm.org/charmm/).
## Preparing code input and output file for uploading to NOMAD
## Features
- All input and output files are expected to be in the supplied directory and its subdirectories.
- The parser searches for the main input file for extraction more information of the order of the commands and
input CARDS. The main input file is assumed to hold at least 80% of the commands given to charmm main process.
-`MINI`, `DYNA`, `ENER`, `GETE`, `PRINT`, `OPEN`, `READ`, and `WRITE` commands can be prossesed with this parser.
- Any new `MINI`, `DYNA`, `ENER`, `GETE` commands are assumed to be a new simulation and each simulation is given in a new [section\_run](https://metainfo.nomad-coe.eu/nomadmetainfo_public/index.html#/public/section_run) in standardized meta information of NOMAD.
- Parser can extract topology information from **PSF**, **RTF**, **PAR** files and CARDS through MDDataAccess package.
-**SEQ** CARDS can be read only for additional information if topology information is not complete.
- Additional topology information can also be extracted from **COOR**, **CRD** files(ascii) and CARDS.
- Input and output coordinates are mainly extracted from both ascii and binary **COOR** and **CRD** files/CARDS and
`PRINT COOR` commands.
...The coordinate information of the most recent command before any given command in the second item of this list is assumed to be the input coordinates of the simulation. Similarly, the next `PRINT`, `WRITE` command after each simulation is also assumed to be the output coordinates if trajectory data (`IUNCRD` or `IUNWRI` units) are missing.
- Trajectory of the simulations are also accessed through MDDataAccess package of [python-common](https://gitlab.rzg.mpg.de/nomad-lab/python-common).
NOMAD accepts `.zip` and `.tar.gz` archives as uploads. Each upload can contain arbitrary
files and directories. NOMAD will automatically try to choose the right parser for you files.
For each parser (i.e. for each supported code) there is one type of file that the respective
parser can recognize. We call these files `mainfiles` as they typically are the main
output file a code. For each `mainfile` that NOMAD discovers it will create an entry
in the database that users can search, view, and download. NOMAD will associate all files
in the same directory as files that also belong to that entry. Parsers
might also read information from these auxillary files. This way you can add more files
to an entry, even if the respective parser/code might not directly support it.
## Download and Installation
The official version lives at:
For charmm please provide at least the files from this table if applicable to your
calculations (remember that you can provide more files if you want):