CHARMM c28a3 install.doc

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                      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 *note Develop: (developer.doc). 

* Menu:

* Contents::      List of Contents of the current release
* Machines::      Machines supported
* Install::       Installation Procedure
* Documentation:: CHARMM Documentation via emacs INFO program
* TOPPAR::        Standard CHARMM Topology and Parameter Files
* UserForm::      CHARMM User Group support

File: Install ]-[ Node: Contents
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                          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

  ~/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

                           Standard RTF/PARAM files distributed with
                           CHARMM 22g2, 22g3, 22g4, 23a1 and 23f1

                           Standard RTF/PARAM files distributed with
                           CHARMM 22g5, 23a2 and 23f2

                           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

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                      Supported Machine Platforms

The current release version is available on the following platforms.

       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
       Intel iPSC Hypercube
       Silicon Graphics

See parallel.doc for details on parallel versions.

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                      User Site CHARMM Installation

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

      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, ' 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
  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.

File: Install ]-[ Node: Documentation
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                          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, 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: (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 ]-[
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: (charmm.doc). CHARMM Documentation
* Emacs: (emacs).              Yours truly
* Info: (info).                This documentation browsing system.

(3) 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

File: Install ]-[ Node: TOPPAR
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                Standard CHARMM Topology and Parameter Files

(A) Topology files
    (1) top_all22_lipid.inp      all hydrogen RTF for lipids
    (2) top_all22_prot.inp       all hydrogen RTF for proteins
    (3) top_all22_na.inp         all hydrogen RTF for nucleic acids
    (4) top_all22_prot_na.inp    all hydrogen RTF for proteins and
                                                      nucleic acids 
    (5) top_all22_model.inp      all hydrogen RTF for protein model cmpds
    (6) toph19.inp               extended atom RTF for proteins
    (7) toprna10r_22.inp         extended atom RTF for nucleic acids

(B) Parameter files
    (1) par_all22_lipid.inp      all hydrogen parameters for lipids
    (2) par_all22_prot.inp       all hydrogen parameters for proteins
    (3) par_all22_na.inp         all hydrogen parameters for nucleic acids
    (5) par_all22_prot_na.inp    all hydrogen parameters for proteins and
                                                             nucleic acids 
    (6) param19.inp              extended atom parameters for proteins
    (7) 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 ADM Jr., July, 1995

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                      CHARMM User Group Support

We maintain the CHARMM user group bulletin board on the network mail
system.  Send your comments to  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

    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

CHARMM .doc Homepage

Information and HTML Formatting Courtesy of:

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