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CHARMM specifications

Information


Unique identifier OMICS_27566
Name CHARMM
Alternative name Chemistry at HARvard Macromolecular Mechanics
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Advanced
Version 42
Stability Stable
Registration required Yes
Maintained Yes

Subtools


  • CHARMM-GUI
  • CHARMMing

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Versioning


No version available

Documentation


Maintainer


  • person_outline CHARMM Team

Additional information


A freely-available reduced version called charmm is available to individuals for non-profit use and a commercial version, called CHARMm is also available. https://www.charmmtutorial.org/index.php/CHARMM_Tutorial

Publications for Chemistry at HARvard Macromolecular Mechanics

CHARMM citations

 (812)
call_split

A1603P and K1617del, Mutations in β Cardiac Myosin Heavy Chain that Cause Laing Early Onset Distal Myopathy, Affect Secondary Structure and Filament Formation In Vitro and In Vivo

2018
J Mol Biol
PMCID: 5958240
PMID: 29660325
DOI: 10.1016/j.jmb.2018.04.006
call_split See protocol

[…] performed on shorter segments of this same part of the β-MHC coiled coil for which experimental atomic structures are available . For these, the N-terminal globular Xrcc4 moieties were removed using CHARMM-GUI . Specifically, sequence 1562–1608 was taken from 5CJ4 (chain A: residues 1562–1615 and chain B: residues 1562–1608, ; sequence 1590–1657 was taken from 5CHX , and sequence 1631–1689 was ta […]

library_books

Cyclization Reaction Catalyzed by Cyclodipeptide Synthases Relies on a Conserved Tyrosine Residue

2018
Sci Rep
PMCID: 5935735
PMID: 29728603
DOI: 10.1038/s41598-018-25479-5

[…] k atoms were constrained at their corresponding optimized geometries from the HEBS profile. CHELP charges, computed with the TPSS/def2-TZVP DFT-D3 method, were used for the atoms in the QM region and CHARMM27 charges for those in the MM region.MD simulations were performed at constant room temperature and pressure for 1 nanosecond for each replica of the HEBS profiles giving 20 ns of the simulatio […]

library_books

QM/MM free energy Simulations of an efficient Gluten Hydrolase (Kuma030) Implicate for a Reactant State Based Protein Design Strategy for General Acid/Base Catalysis

2018
Sci Rep
PMCID: 5935664
PMID: 29728674
DOI: 10.1038/s41598-018-25471-z

[…] ma010 in order to build Kuma030. The model of wild type kumamolisin As-substrate complex were from our previously study.Hydrogen atoms of enzyme-substrate complexes were added by the HBUILD module of CHARMM. The protonation states of acidic and basic residues were determined under pH 4.0 condition depending on surrounding environment. All protonation states are confirmed by H++. Using the Oγ atom […]

library_books

In silico assessment of the conduction mechanism of the Ryanodine Receptor 1 reveals previously unknown exit pathways

2018
Sci Rep
PMCID: 5932038
PMID: 29720700
DOI: 10.1038/s41598-018-25061-z

[…] All MD simulations were carried out using the software package Gromacs 5.1– and the CHARMM36 force field–. The system was propagated in time using the leap frog integrator with a time step of 2 fs, with the only exception being the first equilibration run, in which a reduced time ste […]

library_books

Dynamic tuneable G protein coupled receptor monomer dimer populations

2018
Nat Commun
PMCID: 5923235
PMID: 29703992
DOI: 10.1038/s41467-018-03727-6

[…] Using the CHARMM-GUI Martini webserver, the seven dimer models were converted to coarse grained (CG) representation and embedded in a BPL mimicking membrane composed of POPC:POPS:POPE:cholesterol (15:22:39:24), […]

library_books

Computationally identified novel agonists for GPRC6A

2018
PLoS One
PMCID: 5912754
PMID: 29684031
DOI: 10.1371/journal.pone.0195980

[…] h ten side chain conformers per main chain model were generated for the template using the MOE-2013 (Molecular Operating Environment, 2013.08; Chemical Computing Group, Inc) homology facility and the CHARMM27 force-field [] implemented within MOE. The best-scoring homology model based on Coulomb and Generalized Born interaction energies (GB/VI) scores [] was selected for further MD and docking stu […]

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