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Topic: CHARMM

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	National Partnership for Advanced Computational Infrastructure: Archives
		CHARMM development began in the research group of Professor Martin Karplus at Harvard University.
		CHARMM is maintained and supported on NPACI machines through the efforts of the Molecular Sciences Thrust Area, and is available to all licensed CHARMM users by contacting Professor Charles L.
		CHARMm (the commercial version of CHARMM) is available to scientists in industry, and academic researchers who wish to have full user support, through MSI.
	www.npaci.edu /Resources/SciComp/Applications/CHARMM (0 words)

	Reference.com/Encyclopedia/CHARMM
		CHARMM (Chemistry at HARvard Macromolecular Mechanics) is the name of a widely used set of force fields for molecular dynamics as well as the name for the molecular dynamics simulation and analysis package associated with them.
		The CHARMM Development Project involves a network of developers throughout the world working with Martin Karplus and his group at Harvard to develop and maintain the CHARMM program.
		CHARMM originated at Martin Karplus's group at Harvard.
	www.reference.com /browse/wiki/CHARMM (741 words)

	contact map instructions
		CHARMM determines the center of geometry for each residue and then can give you a list of residues which are in contact.
		CHARMM does not seem to mind the fact that the line numbers are changed by this fix.
		Check the output of CHARMM for any warnings indicating that it could not find coordinates for a particular atom or that no parameters could be found for a particular atom.
	structbio.vanderbilt.edu /chazin/wisdom/cmap_instruct.html (1852 words)

	[No title] (Site not responding. Last check: )
		CHARMM input files are prepared by the script and CHARMM jobs are dispatched to a queuing system.
		Mcharmm_c28a3 charmm These are not included with this distribution and have to be obtained from the CHARMM developers.
		The MARKOV chain of accepted generations are listed in the "sampling_tps" and "sampling_bolas" files and are used to compute Monte Carlo averages of conformational variables, autocorrelation functions etc. The "race_history.log_*" files are log files of the runs and are used to verify consistency and debugging of the PERL script.
	monod.biomath.nyu.edu /~rradhak/bolas/README (1144 words)

	[No title]
		CHARMm CHARMm is a general and flexible software application for modelling the structure and behavior of molecular systems.
		CHARMm also provides great flexibility: in addition to building molecular structures that can be displayed using the HYDRA graphical display system, CHARMm uses an empirical energy function for energy minimization, molecular dynamics simulation, or vibrational analysis.
		Given the CHARMm calculated empirical energy field, molecular dynamics simulations are performed by classical mechanics in which the equations of motion derived from Newton's second law are solved for all atoms in the molecule.
	www.ibiblio.org /pharmacy/Mml/charmm.html (820 words)

	CHARMM
		The CHARMM Development Project involves a network of developers in the
		United States and elsewhere working with Professor Karplus and his group
		at Harvard to develop and maintain the CHARMM program.
	www.charmm.org (39 words)

	Documentation Overview
		The Harvard designation for this version is c29b2, where "c" refers to CHARMM, 29 is the version number and the letters g, b or a indicate the release, i.e.
		In fact, several parts of CHARMM are under active development, and there are significant enhancements since the previous versions were released.
		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.).
	www.uwm.edu /People/dxie/Charmm/c29b2/Overview.Html (655 words)

	CHARMm Tutorial
		A CHARMm script can be written in any text editing processor, such as vi, as long as it can be saved in a "text only" format.
		Next, CHARMm is expecting to read in the topology files and the parameter file.
		As a final note, be aware that you can add comments to your CHARMm scripts as long as the line the comment is on begins with an exclamation mark.
	cmm.info.nih.gov /modeling/guide_documents/kyle/kyle1.html (1028 words)

	CHARMm Principles - Setting Constraints and Periodic Boundaries
		In CHARMm, a variety of options can help you tailor your files and data to focus on the parts of a system in which you are interested.
		CHARMm uses a harmonic potential to restrict the motion of a dihedral angle usually to a value close to a reference position.
		The CHARMm image facility already enables energies of crystals to be calculated, but the input required to use the facility is often difficult and cumbersome to set up.
	www.scripps.edu /rc/softwaredocs/msi/quanta98/charmm/Ch05_constraints.FM5.html (3460 words)

	Frequently Asked Questions (Site not responding. Last check: )
		This is not saying that Charmm will use all of your memory (it won't), but it gives us a little bit more space to do our simulations correctly and without errors.
		Charmm is an interpreter for a protein-ligand docking model that we specify in an input file called charmm.inp.
		This means that Charmm is continuously reading lines from this file so that it can do the calculations we ask it to perform.
	docking.utep.edu /faq.php (1620 words)

	c29a1 charmmrate.doc
		The charmm program is the main driver of the integrated program, which makes a FORTRAN call to the interface subprogram, charmmrate, to initiate VTST calculations by polyrate.
		The energy and energy gradients for the primary-zone atoms required by polyrate are determined by charmm through the interface subprogram and are supplied to polyrate through a set of subroutines called the polyrate hooks.
		In addition to the CHARMM topology and parameter files, the cr02.crd file is required, which contains the instantaneous (initial) coordinates of chorismate in water from a molecular dynamics simulation.
	www.dtc.umn.edu /~duany/charmm_doc/charmmrate.html (3712 words)

	Computational Chemistry at NCSA - CHARMm
		CHARMM (Harvard version) is a general purpose molecular mechanics, molecular dynamics and vibrational analysis packages for modelling and simulation of the structure and behavior of molecular systems from an individual organic molecule to a large oligomeric protein in its solvent environment.
		To access CHARMM at NCSA, you have to obtain an authorization letter from Prof.
		The current version that is supported at NCSA is CHARMM 29b2 and available on the IBM p690 (copper), the IBM xSeries 330 (platinum), and the Xeon Cluster (tungsten).
	www.ncsa.uiuc.edu /UserInfo/Resources/Software/CHEM/charmm.html (101 words)

	Accelrys: CHARMm for molecular mechanics and molecular dynamics simulation
		CHARMm (Chemistry at HARvard Macromolecular Mechanics) provides a vast range of functionality for molecular mechanics and molecular dynamics simulation that has been developed by leading scientists across the world.
		CHARMm functionality can be applied to diverse areas of research, including protein modeling, structure-based design, structural biology, and nanotechnology.
		New in CHARMm 32b1 (June 2006): Includes a command line typing tool to type thousands of ligands in batch mode.
	www.accelrys.com /products/charmm (162 words)

	Simulaid documentation
		Once the list of residues and atoms are known to Amber or Charmm, they will turn to their RTF file where the combination of residue names and atomnames will provide for each atom their atomtypes and partial charges.
		Charmm uses an additional file of the type.img that specifies the centers of all surrounding cells, but most packages use built-in routines for the different cell types allowed.
		For Charmm format output, the segment id of the additional structures will be appended by 1,2, etc., as long as there is 'room' for this additional information in the four-digit sequence id (i.e., the original segment id contained enough blanks).
	fulcrum.physbio.mssm.edu /~mezei/simulaid/simulaid.html (6725 words)

	Documentation - CHARMM.pm
		The CHARMM package is used to run CHARMM through a perl interface.
		A log file for CHARMM output and a command log file for commands sent to CHARMM may be given as an option.
		The arguments are a force constant, a CHARMM selection expression and flags whether to keep previous coordinates and whether to use coordinates from the alternate coordinate set
	mmtsb.scripps.edu /doc/CHARMM.pm.html (1258 words)

	Computational Chemistry - CHARMM Water Tutorial
		CHARMM can be used in interactive mode by starting the program and typing commands into the interpreter, much like in an interpreted computer programming language.
		This is the only place in the CHARMM script where you actually need to pay attention to which column you are typing in.
		This line tells CHARMM that we are defining a residue (RESI), named H2O, and that this residue has an overall charge of 0.0.
	persweb.wabash.edu /facstaff/fellers/tutorial/water_tutorial/page_1.html (1019 words)

	[No title]
		CHARMM Element doc/developer.doc 1.4 File: Develop, Node: Top, Up: (chmdoc/charmm.doc), Previous: (c22doc/testcase.doc), Next: (c22doc/changelog.doc) CHARMM Developer Guide This is to provide a guide to someone who wants to understand how CHARMM is implemented, and a variety of rules that should be followed by anyone who wishes to modify it.
		CHARMM 23f2 and later versions are fully in FORTRAN except some machine specific codes written in the C language.
		CHARMM tools are utility programs/procedures for installation, modification, optimization, etc. In ~/charmm/tool, we include the preprocessor PREFX and utility procedures for module makefile generation.
	www.chm.tu-dresden.de /edv/charmm/developer.doc (3515 words)

	institute for computational biomedicine: CHARMM
		CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a program for performing molecular dynamics and mechanics computations.
		CHARMM may be used for energy minimization, normal mode analysis, chemical and conformational free energy analysis, and a variety of other computations as well.
		The force field typically used with CHARMM is parameterized for proteins, nucleic acids and lipids.
	icb.med.cornell.edu /crt/CHARMM/index.xml (329 words)

	Charmm Notes
		A CHARMM benchmark ftp directory is avaliable under the Harvard CHARMM page.
		The latter appears to be the approach of commercial (MSI) CHARMm.
		THis job is a test case for the QM/MM interface using, this time, GAMESS-UK as the QM program, and again CHARMM for the MM side.
	www.geocities.com /gschreckenbach/charmm_DIR/charmm.html (1595 words)

	CHARMM Empirical Force Fields
		This change was motivated by the ever increasing complexity of the topology and parameter files due to the inclusion of additional model compounds.
		Topology and parameter files for the AMBER, OPLS and BMS force fields are now included, allowing for modeling studies with CHARMM using these force fields.
		An overview of the parameter optimization approaches to extend the CHARMM force fields may be found in the following references or in MacKerell, A.D., Jr.
	www.pharmacy.umaryland.edu /faculty/amackere/force_fields.htm (643 words)

	CHARMM Project: Protein Folding and Misfolding
		In order to use CHARMM, a research group needs to obtain a license before access to this software is granted.
		Parallelization of CHARMM on a LINUX-PC Cluster (ETHZ)
		CHARMM: The Energy Function and Its Parameterization with an Overview of the Program, in The Encyclopedia of Computational Chemistry, 1, 271-277, P. v.
	www.cscs.ch /~redaelli/docs/CHARMM (567 words)

	CHARMM
		CHARMM models the dynamics and mechanics of macromolecular systems using empirical and mixed empirical/quantum mechanical force fields.
		CHARMM is designed to investigate the structure and dynamics of large molecules.
		It performs free energy calculations of mutations and drug binding as well as conformational folding of peptides.
	www.psc.edu /general/software/packages/charmm/charmm.html (222 words)

	Building Code with PathScale
		CHARMM (Chemistry at HARvard Molecular Mechanics) is a program for macromolecular simulations, including energy minimization, molecular dynamics, and Monte Carlo simulations.
		To build CHARMM, you will need to download the source, apply the provided patches, and then build and test it.
		The source code for the CHARMM program is distributed with documentation to individual academic research groups.
	www.pathscale.com /building_code/charmm.html (252 words)

	CHARMM Documentation Index (Site not responding. Last check: )
		CHARMM version c28n1; NIH mods to c28a1 (1st alpha release of c28)
		CHARMM version c27n1; NIH mods to c27a1 (1st alpha release of c27)
		CHARMM version c26n1; NIH mods to c26a1 (1st alpha release of c26)
	www.lobos.nih.gov /Charmm/chmdoc.html (164 words)

	PGI \| Resources \| CHARMM Tips & Techniques
		This guide was created for Version v30b2 of CHARMM using PGI Compiler Release 5.2 or 6.0 for use on a 32-bit x86 system running Linux.
		Information about CHARMM (Chemistry at HARvard Molecular Mechanics) can be found at the CHARMM Web page.
		Before building the CHARMM executable make sure that your shells "path" variable includes the location of the PGI compilers.
	www.pgroup.com /resources/charmm/charmm_pgi5260_32.htm (206 words)

	CHARMM - Tutorial
		The exercises may also serve as a tutorial on how to use CHARMM though the emphasis is on the principles of the methods, not the details of the functionality provided by the program.
		The CHARMM documentation explains most commands in reasonable detail; however, it is intended as a reference and not as an introduction.
		You can have commands in CHARMM that are longer than one line, but you have to mark that specifically (you need to put a '-' at the end of the line that is continued on the next).
	www.mdy.univie.ac.at /lehre/charmm/course1/course1-1.html (5952 words)

	[No title]
		This value is currently set by CHARMM to be the character representation of the residue number in the segment starting from the first real monomer unit in it.
		When CHARMM is loaded, each atom has associated with it a harmonic force constant initially set to zero.
		The method was brought to CHARMM by Wilfred Van Gunsteren (WFVG), and is referenced in J. Comp.
	fulcrum.physbio.mssm.edu /endo/charmm22 (14534 words)

	CHARMM — CSC
		CHARMm is a general and flexible software application for modelling the structure and behavior of molecular systems.
		A variety of systems, from an individual organic molecule to a large oligomeric protein in its solvent environment, can be simulated.
		You can use CHARMm as a standalone program or within Discovery Studio, InsighII and QUANTA graphical molecular modeling programs.
	www.csc.fi /english/research/software/charmm (113 words)

	CHARMM
		CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a program for macromolecular simulations, including energy minimization, molecular dynamics and Monte Carlo simulations.
		The CHARMM Development Project involves a network of developers in the United States and elsewhere working with Professor Karplus and his group at Harvard to develop and maintain the CHARMM program.
		Describe briefly the kind of research for which you intend to use the CHARMM program and the computers you will be using.
	yuri.harvard.edu (0 words)

	SDSC User Support: SAC: Current Collaborations: CHARMM
		A key bottleneck in making this process economically viable is the slow breakdown of cellulose by the enzyme cellulase, and scientists want to understand this process at the molecular level so that they can target further research to speed up this important reaction.
		To explore the intricate molecular dynamics of this process, the researchers have used the CHARMM (Chemistry at HARvard Molecular Mechanics) code, a versatile community code for simulating biological reactions.
		The research is enabling the largest simulations ever of an important scientific problem that will yield economic and environmental benefits, and in addition, the improvements to the CHARMM code that will continue to be available for the scientific community to use on a wide range of other problems.
	www.sdsc.edu /us/sac/projects/charmm.html (320 words)

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