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Protocols

CHARMM36m specifications

Information


Unique identifier OMICS_14325
Name CHARMM36m
Alternative name Chemistry at HARvard Macromolecular Mechanics 36m
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data CHARMM36 force field in GROMACS format
Input format GRO
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Alexander MacKerell

Publication for Chemistry at HARvard Macromolecular Mechanics 36m

CHARMM36m citations

 (10)
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Clinically relevant mutations in the ABCG2 transporter uncovered by genetic analysis linked to erythrocyte membrane protein expression

2018
Sci Rep
PMCID: 5945641
PMID: 29749379
DOI: 10.1038/s41598-018-25695-z
call_split See protocol

[…] Three 100 ns long MD simulations were performed with the wild type and mutant NBDs using GROMACS with CHARMM36m force field,. For simulation details see the Supplementary materials. Analysis was performed by employing GROMACS tools, VMD Network Wizard Plugin, and the MDAnalysis Python package. […]

library_books

Closely related, yet unique: Distinct homo and heterodimerization patterns of G protein coupled chemokine receptors and their fine tuning by cholesterol

2018
PLoS Comput Biol
PMCID: 5864085
PMID: 29529028
DOI: 10.1371/journal.pcbi.1006062

[…] e final production runs of the dimerization simulations.In the next step, the systems were converted back to atomistic detail using backward [] in order to prepare the system for simulations with the CHARMM36m force field [, ]. Ions were added to reach a salt concentration of 0.15 nM and to set the system net charge to zero. Prepared atomistic systems contained roughly 320 lipids, 21,000 water mol […]

library_books

Repertoire Analysis of Antibody CDR H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification

2018
Front Immunol
PMCID: 5840193
PMID: 29545810
DOI: 10.3389/fimmu.2018.00413

[…] The Fv regions were retrieved from the original PDB files. The MD simulations were performed using the NAMD 2.12 package () with the CHARMM36m force field and the CMAP backbone energy correction (). The truncated Fv structures were solvated with TIP3P water in a rectangular box such that the minimum distance to the edge of the box […]

call_split

Gi and Gs coupled GPCRs show different modes of G protein binding

2018
Proc Natl Acad Sci U S A
PMCID: 5877964
PMID: 29463720
DOI: 10.1073/pnas.1721896115
call_split See protocol

[…] x was inserted into a hydrated POPC bilayer, creating a final system of 231,641 atoms. We performed three unbiased simulations of the prepared rhodopsin–Gi complex with the CHARMM36 force field (with CHARMM36m protein parameters) using the AMBER 16 software suite on graphics processing units (GPUs) (, ). Each of the three simulations was ∼600 ns in length. See SI Materials and Methods for a comple […]

library_books

A “Tug of War” Maintains a Dynamic Protein–Membrane Complex: Molecular Dynamics Simulations of C Raf RBD CRD Bound to K Ras4B at an Anionic Membrane

2018
PMCID: 5832993
PMID: 29532030
DOI: 10.1021/acscentsci.7b00593

[…] in refs (, , , )). Five independent simulations were performed each for 1 μs. Umbrella sampling simulations were performed to calculate the free energy of CRD and K-Ras4B binding to the membrane. The CHARMM36m force field was used in all simulations and energy calculations. […]

library_books

Balancing Force Field Protein–Lipid Interactions To Capture Transmembrane Helix–Helix Association

2018
J Chem Theory Comput
PMCID: 5852462
PMID: 29424543
DOI: 10.1021/acs.jctc.7b00983

[…] ly, we considered whether the dimer instability was specific to the CHARMM36 force field or was also found in other force fields. A similar result is obtained with the recently published modification CHARMM36m. Another widely used lipid force field is the AMBER Slipids model., We find that combining Amber ff03w with Slipids seems slightly more stable but still results in dissociation after about 2 […]


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CHARMM36m institution(s)
Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA; Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
CHARMM36m funding source(s)
This work was supported by the NIH (GM072558) and (GM084953) and computational support from the University of Maryland Computer-Aided Drug Design Center, XSEDE (TG-MCA98N017) and (TG-MCB090003) and the SuperMUC supercomputer at the Leibniz Rechenzentrum.

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