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