Overview of CHARMM version c28a3 .doc Files

Protein A animation


The documentation presented here is that for the latest academic version of the CHARMM program (Chemistry at HARvard Molecular Mechanics), as maintained at the TSRI development site. Quite a few features are contained in this version that are NOT included in the CHARMm version distributed by MSI as part of the Quanta package. The information in these .doc files has been contributed by CHARMM developers over the years, and hopefully reflects the current state of the program. The Harvard designation for this version is c28a3, where "c" refers to CHARMM, 28 is the version number and the letters g, b or a indicate the release, i.e. gamma, beta or alpha; Note releases of gamma and beta codes at TSRI may contain a few bugfixes and other minor differences and alpha level codes are development versions.

The compiled program itself is available on several computer systems at TSRI (HP clusters - hpux, SGI machines - sgi, and MPP machines - SPP1000, TMC/GWS/Sun) and this documentation is largely meant as an on-line usage guide for people using CHARMM on these systems. At present it is more of a reference manual than a tutorial, although although someday material from the CHARMM lectures, developed initally in the Karplus Group in the early '80s and expanded by BR Brooks (DCRT/LSB), will be added to these WWW pages.

CHARMM remains essentially a command line program, i.e. a command is read from the input stream (typed, or from a file) and acted upon. Even the X11/GL graphics function this way, although that part may change over the next year or so. In fact, several parts of CHARMM are under active development, and there are significant enhancements since the previous versions were released. Consequently, there will be periodic changes and additions to the documentation offered here.

Running CHARMM Under Unix

While CHARMM may be run interactively, that is not usually recommended, except for graphics; even then, a stream file should be used for the initial setup (reading PSF, coords, etc.). The general syntax for using the program (assuming /bin/csh) is:

charmm < filename.inp >& filename.out [[param:value] ...] [ & ]

The actual name of the program (or script which runs the program) on the computer system being used; the name may not be the same on all systems.
A text file containing CHARMM input commands, using the command syntax described in usage.doc. The actual filename is up to the user, although it is useful to use short names which hint at the overall purpose, e.g. makpsf.inp
The log file for the CHARMM run, containing echoed commands, and various amounts of command output. The output print level may be increased or decreased in general, and procedures such as minimization and dynamics have printout frequency specifications.
CHARMM script parameters (essentially user defined variables) may optionally be defined on Unix shell command line, using the form param:value; the value is substituted for occurrences of @param in the input script.
The optional ampersand will place the program in the background under most Unix shells; note that the computer system being used may have a batch job queueing system which should normally be used instead of running CHARMM as a background process via the above syntax.

Consult the local system administrator to determine the actual program name (e.g. charmm, charmm24, etc.) and the policy for running compute intensive tasks (batch queue, background, etc.) on the computer system being used. In general, CHARMM calculations are best limited to around 12 to 16 hours, to both promote resource sharing and to minimize data loss due to machine or network failures.

For foreground usage, e.g. graphics, start the program by typing it's name alone, wait for the program "header" to be printed, and enter a title. Then use a "stream" file, e.g.

stream psf-crd.str

will read CHARMM commands from the file named psf-crd.str as if they were being typed at the keyboard; as implied by the name, the stream file reads the PSF, PARAms, COORdinates, etc., the basic starting point for all work with CHARMM.

CHARMM .doc Homepage

Information and HTML pages provided by:

NIH/DCRT Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory
Modified, updated and generalized by C.L. Brooks, III
The Scripps Research Institute

Documentation Overview / rvenable@deimos.cber.nih.gov / brooks@scripps.edu