CHARMM pipeline

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

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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

CHARMM IN pipelines

 (24)
2018
PMCID: 5923327
PMID: 29670004
DOI: 10.3390/toxins10040161

[…] [39]. pdb files were visualized using usfc chimera software (version 1.8.1, san francisco, ca, usa, 2013) [40]., for the molecular dynamics simulations, the amidated model topologies were defined by charmm27 force field [41]. the simulations were performed using gromacs 5.1.4 software (san francisco, ca, usa, 2016) [42] with the water explicit model tip3p and with 50%tfe solution. the models […]

2017
PMCID: 5519381
PMID: 28592485
DOI: 10.1074/jbc.M117.789446

[…] dynamics simulations were performed at a constant temperature of 310 k and a constant pressure of 1 bar, using gromacs version 5.0.4 (74), using previously reported protocols (30). using the charmm-gui (75–77) input generator, we embedded the protein molecule (pagp crystal structure, pdb code 1thq (26)) in a micelle system consisting of 80 dpc molecules. we first equilibrated […]

2017
PMCID: 5669090
PMID: 29142407
DOI: 10.4103/pm.pm_195_16

[…] using the cdocker protocol under the protein–ligand interaction section in discovery studio® 3.1 (accelrys, san diego, usa). in general, cdocker is a grid-based molecular docking method that employs charmm force fields. protein was first held rigid while the ligands were allowed to flex during the refinement. two hundred random ligand conformations were then generated from the initial ligand […]

2016
PMCID: 4718466
PMID: 26784025
DOI: 10.1371/journal.pone.0147190

[…] (md) simulations of btk in complex with the final hit compounds obtained from docking studies and the most active compound from the training set were performed using gromacs 4.5.7 package with charmm27 force field [38]. topology files for ligands were generated by swissparam [39]. the system were solvated in a dodecahedron box containing tip3p water model to form an aqueous environment […]

2016
PMCID: 4791994
PMID: 27041853
DOI: 10.4103/0973-1296.176111

[…] using the cdocker protocol under the protein-ligand interaction section in discovery studio® 3.1 (accelrys, san diego, usa). in general, cdocker is a grid-based molecular docking method that employs charmm force fields. a protein was firstly held rigid while the ligands were allowed to flex during the refinement. two hundred random ligand conformations were then generated from the initial ligand […]

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