CHARMM

Table Of Contents

Previous topic

Benchmark | g77/RH-6.0 | g77*/Debian| f2c/Debian | pgf77 | f77/Absoft

Next topic

CHARMM Testcases

This Page

CHARMM Release and Installation

This document contains a formal definition of the current CHARMM release followed by a detailed installation procedure. We concern here features and end-line-user-site installation. Issues regarding developer sites are documented in CHARMM Developer Guide.

CHARMM Release Package

The CHARMM release package for CHARMM developers and user sites includes

  1. complete source and include files,
  2. updated documentation files,
  3. some supporting data files,
  4. testcases,
  5. the PREFX preprocessor and tools needed to set up CHARMM development environments and
  6. standard topology and parameter files.

The files are organized in the followoing subdirectories. ~/ denotes the directory where you have unpacked (read from a tape drive or issued the UNIX tar command) the CHARMM release package delivered to you. In ~/cnnXm, nn is the version number, X is the version trunk designator (a for alpha or developmental, b for beta release and c for gamma or general release) and m is the revision number. For example, c24b1 is CHARMM version 24 beta release revision 1.

~/cnnXm/ The main directory of CHARMM
~/cnnXm/source/ Contains all CHARMM source files
~/cnnXm/doc/ The most recent CHARMM documentation If GNU emacs is available on your host machine, you may ‘soft’ link this directory to the emacs info directory to access the documentation via the emacs info-program.
~/cnnXm/support/ Supplementary programs and data files
~/cnnXm/support/MMFF/ MMFF parameter files
~/cnnXm/support/aspara/ Atom Solvation Parameter files and testcases
~/cnnXm/support/bpot/ CHARMM support data files 18 spherical deformable boundary potential files for the TIP3P water oxygen.
~/cnnXm/support/form/ problem, bug, and development report forms
~/cnnXm/support/htmldoc/ doc to HTML conversion utilities
~/cnnXm/support/imtran/ CHARMM support data files 4 image transformation files for periodic boundary simulations
~/cnnXm/support/membrane lipid membrane construction protocol
~/cnnXm/test/ CHARMM testcases
~/cnnXm/tool/ Preprocessor, FLECS translator and other CHARMM installation utilities
~/cnnXm/topar/ Standard topology/parameter files
~/cnnXm/toppar/toppar_history/c22g2_g3_g4_c23a1__f1 Standard RTF/PARAM files distributed with CHARMM 22g2, 22g3, 22g4, 23a1 and 23f1
~/cnnXm/toppar/toppar_history/c22g5_c23a2_f2 Standard RTF/PARAM files distributed with CHARMM 22g5, 23a2 and 23f2
~/cnnXm/toppar/toppar_history/c23f3_f4_f5_c24a1_a2_a3 Standard RTF/PARAM files distributed with CHARMM 23f3, 23f4, 23f5, 24a1 and 24a3
~/cnnXm/exec/ The CHARMM executable charmm will be stored here when installation is completed.
~/cnnXm/build/ Contains Makefile, module makefiles and the log file of the install make command for each machine in the subdirectory named after the machine type.
~/cnnXm/lib/ Contains library files

Supported Machine Platforms

The current release version is available on the following platforms.

  • Alliant
  • Apollo
  • Convex
  • Cray X-MP, Cray Y-MP and Cray-2
  • DEC Stations running Ultrix
  • DEC Alpha Stations running OSF
  • Hewlett-Packard Apollo 700 Series
  • IBM-3090 running AIX
  • IBM-RS/6000
  • Intel iPSC Hypercube
  • Silicon Graphics
  • Sun

See Benchmark | g77/RH-6.0 | g77*/Debian| f2c/Debian | pgf77 | f77/Absoft for details on parallel versions.

User Site CHARMM Installation

The installation is carried out by the shell script ~/cnnXm/install.com. Change your working directory to ~/cnnXm and run install.com. install.com expects one or more arguments.

install.com <host_machine_type> [ <CHARMM_size> <install switches> ]

The default and possible arguments are

<host_machine_type1> = { alpha, alphamp, cm5, convex, cray, cspp }
                       { dec, gnu, gws, hal, hpux, ibmrs, ibmsp  }
                       { intel, sgi, stardent, sun, t3d, terra   }

<CHARMM_size>        = { reduced, small, medium, large  | medium }

<install switches>   = { 1, 2, FULL, LITE, F77, G77, P, M, S, 64 }
                       { Q, C, X, G                              }

where { | } is for { possible arguments | default }. <CHARMM_size> depends on your machine memory configuration. In general, ‘medium’ is recommended. User site installation can be taylored with the install.com switches.

   1  to halt after setting up installation directory.
   2  to halt after making installation utilities.
FULL  For FULL featured version (default).
LITE  For a version with reduced functional features.
 F77  Uses Absoft/Linux (default: f2c driven by fort77).
 G77  Uses g77/Linux (default: f2c driven by fort77).
   P  links to PVM
   M  links to MPI
   S  Uses TCP/IP SOCKET library for parallel.
  64  to compile in the 64-bit mode on SGI platforms.
   Q  replace QUANTUM with GAMESS.
   C  replace QUANTUM with CADPAC.
   X  for the X-lib graphics to be included.
   G  for the GL-lib graphics to be included.

When one or more install switches are used, <CHARMM_size> must be specified too. Note that X and G are mutually exclusive and G requires the GL library. P and M are also mutually exclusive. The switch 2 can be used to stop installation and modify the pref.dat file to further customize CHARMM features.

For example, ‘install.com sgi’

  1. installs the preprocessor PREFX in ~/cnnXm/tool (prefx_sgi),
  2. generates the proper ~/cnnXm/build/sgi/pref.dat file (PREFX data file),
  3. generates makefile suitable for SGI computers running under IRIX (~/cnnXm/build/sgi/Makefile),
  4. processes FORTRAN and C source files, compiles and builds module libraries in ~/cnnXm/lib/sgi, and
  5. links them to produce the executable ~/cnnXm/exec/sgi/charmm.

CHARMM Documentation

The CHARMM documentation set is being updated and improved. The up-to-the-date documentation set is included in the current release. The documentation is an integral part of CHARMM.

The documentation files are accessible through the info program in GNU emacs. If emacs is available on your system, you may incorporate the documentation into the info-tree structure. The following is the info-building procedure.

  1. Locate the info directory. On tammy.harvard.edu, it is /usr/lib/gemacs/info. It may differ on your machine.
  2. Find the file, dir, in the info directory. You should have a write access of the directory. If the info directory is protected, contact your system manager and let him do the job. Edit the dir file and insert the following one line under “* Menu”.
* CHARMM: (chmdoc/charmm.doc). CHARMM Documentation

It should appear exactly as shown; asterisk (*) in the first column, etc. The the part of dir file may look like this.

File: dir       Node: Top       This is the top of the INFO tree

        Quick Key Reference

        d                  return here
        q                  exit
        ?                  list INFO commands
        h                  help
        mCHARMM<return>    go into CHARMM documentation
        1                  go into CHARMM documentation (works for 1..5)
        u                  go up

===========================================================================
* Menu:

* CHARMM: (chmdoc/charmm.doc). CHARMM Documentation
* Emacs: (emacs).              Yours truly
* Info: (info).                This documentation browsing system.
  1. Save the file and exit the editor. You now have to link the CHARMM documentation directory as in the following.

    ln -s ~/cnnXm/doc chmdoc

    Remember that ~/ is the parent directory that holds the charmm directory.

Standard CHARMM Topology and Parameter Files

  1. Topology files

    top_all22_lipid.inp

    all hydrogen RTF for lipids

    top_all22_prot.inp

    all hydrogen RTF for proteins

    top_all22_na.inp

    all hydrogen RTF for nucleic acids

    top_all22_prot_na.inp

    all hydrogen RTF for proteins and nucleic acids

    top_all22_model.inp

    all hydrogen RTF for protein model cmpds

    toph19.inp

    extended atom RTF for proteins

    toprna10r_22.inp

    extended atom RTF for nucleic acids

  2. Parameter files ======================= =========================================== par_all22_lipid.inp all hydrogen parameters for lipids par_all22_prot.inp all hydrogen parameters for proteins par_all22_na.inp all hydrogen parameters for nucleic acids par_all22_prot_na.inp all hydrogen parameters for proteins and

    nucleic acids

    param19.inp extended atom parameters for proteins pardna10_22.inp extended atom parameters for nucleic acids ======================= ===========================================

The CHARMM22 all-hydrogen topology and parameter sets may be considered to be stable, however, further changes cannot be excluded. The bulk of the changes are expected to be additions leading to an expanding set of parameters which are compatible across proteins, nucleic acids, lipids, and, ultimately, carbohydrates. The carbohydrate parameter work is still in progress by John Brady and coworkers. See the file toppar_all.history for a listing changes in the files over time. top_all22_model.inp includes the majority of model compounds used in the protein parameterization and is to be used in conjunction with par_all22_prot.inp. top_all22_prot_na.inp and par_all22_prot_na.inp contain both the protein and nucleic acid parameters allowing for calculations on protein-nucleic acid complexes. The lipid parameters may be combined in a similar fashion, although it hasn’t been performed at present. The extended atom parameters for proteins are the same as those included with CHARMM20 which are based on Wally Reiher’s thesis. For the extended atom nucleic acid parameters those of Nilsson and Karplus, J. Comp. Chem. 7:591-616, 1986 are used which were also included in the CHARMM20 release and are the only set to include explicit hydrogen bonding terms. Some alterations of the extended atom nucleic acid topology and parameter files have been made in order to maintain compatibility with the multiple dihedral scheme in CHARMM22. Please send all remarks and suggestions to alex@mmiris.ab.umd.edu. ADM Jr., July, 1995

CHARMM User Group Support

We maintain the CHARMM user group bulletin board on the network mail system. Send your comments to charmm-users@tammy.harvard.edu. If you wish to receive CHARMM user group messages, let the CHARMM manager know. Your comments can include

  1. suggestions for improvements,
  2. tricks you discovered,
  3. work around for bugs,
  4. remedy for somebody else’s problem, and
  5. anything you want to say about CHARMM.

Problems and bugfixes should be reported to CHARMM developers. Send your reports to charmm-bugs@tammy.harvard.edu.

Your problem description should include

  1. exactly which command is malfunctioning,
  2. what options you are using,
  3. a sample input containing only a few lines to isolate the problem, and
  4. your verbal description of the problem.

Your bugfix report should include

  1. the problem you had,
  2. cause of the problem,
  3. how you traced to the cause,
  4. how you corrected it,
  5. any side effects, and
  6. your comments.

You may find the forms, problem.form and bugfix.form in the support/form directory useful in reporting problems and bugfixes.

If you have questions/comments/suggestions about CHARMM management, send your remark to chmgr@tammy.harvard.edu.