The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
CHARMM-GUI supports the Amber force fields
Abstract
As part of our ongoing efforts to support diverse force fields and simulation programs in CHARMM-GUI, this work presents the development of FF-Converter to prepare Amber simulation inputs with various Amber force fields within the current CHARMM-GUI workflow. The currently supported Amber force fields are ff14SB/ff19SB (protein), Bsc1 (DNA), OL3 (RNA), GLYCAM06 (carbohydrate), Lipid17 (lipid), GAFF/GAFF2 (small molecule), TIP3P/TIP4P-EW/OPC (water), and 12-6-4 ions, and more will be added if necessary. The robustness and usefulness of this new CHARMM-GUI extension are demonstrated by two exemplary systems: a protein/N-glycan/ligand/membrane system and a protein/DNA/RNA system. Currently, CHARMM-GUI supports the Amber force fields only for the Amber program, but we will expand the FF-Converter functionality to support other simulation programs that support the Amber force fields.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
VMD: visual molecular dynamics
Humphrey, W., Dalke, A., & Schulten, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00018-5 · Cited by 66,952
Fast Parallel Algorithms for Short-Range Molecular Dynamics
Plimpton, S. (1995) · Journal of Computational Physics · doi:10.1006/jcph.1995.1039 · Cited by 44,721
Scalable molecular dynamics with NAMD
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20289 · Cited by 16,914
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
Eastman, P., Swails, J., Chodera, J. D., McGibbon, R. T., Zhao, Y., Beauchamp, K. A., Wang, L.-P., Simmonett, A. C., Harrigan, M. P., Stern, C. D., et al. (2017) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1005659 · Cited by 2,748
Neurosteroids: endogenous regulators of the GABAA receptor
Belelli, D., & Lambert, J. J. (2005) · Nature reviews. Neuroscience · doi:10.1038/nrn1703 · Cited by 1,159
Hsu, P., Bruininks, B. M. H., Jefferies, D., Cesar Telles de Souza, P., Lee, J., Patel, D. S., Marrink, S. J., Qi, Y., Khalid, S., & Im, W. (2017) · Journal of Computational Chemistry · doi:10.1002/jcc.24895 · Cited by 202
Self-citation
Cited by
CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed
Hwang, W., Austin, S. L., Blondel, A., Boittier, E. D., Boresch, S., Buck, M., Buckner, J., Caflisch, A., Chang, H.-T., Cheng, X., et al. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.4c04100 · Cited by 136
Self-citationLong, T., Li, D., Vale, G., Jiang, Y., Schmiege, P., Yang, Z. J., McDonald, J. G., & Li, X. (2024) · Cell · doi:10.1016/j.cell.2024.08.004 · Cited by 31
Computational Insights into Membrane Disruption by Cell-Penetrating Peptides
Catalina-Hernandez, E., Aguilella-Arzo, M., Peralvarez-Marin, A., & Lopez-Martin, M. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c01940 · Cited by 18
Pakuła, K., Sequeiros-Borja, C., Biała-Leonhard, W., Pawela, A., Banasiak, J., Bailly, A., Radom, M., Geisler, M., Brezovsky, J., & Jasiński, M. (2023) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-023-04751-6 · Cited by 11
A computational model for lipid-anchored polysaccharide export by the outer membrane protein GfcD
Fruet, C., Martinez-Goikoetxea, M., Merino, F., & Lupas, A. N. (2024) · Biophysical Journal · doi:10.1016/j.bpj.2024.08.012 · Cited by 1
Metadata
- Authors
- Lee, J., Hitzenberger, M., Rieger, M., Kern, N. R., Zacharias, M., & Im, W.
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 2020-07-15
- Volume
- 153
- Issue
- 3
- Pages
- 035103-035103
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W3042908073
- Cited by
- 428
- References
- 6
- FWCI
- 10.23
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: CHARMM-GUI supports the Amber force fields. https://app.cochat.ai/papers/10.1063/5.0012280
- The paper
- Lee, J., Hitzenberger, M., Rieger, M., Kern, N. R., Zacharias, M., & Im, W. (2020). CHARMM-GUI supports the Amber force fields. The Journal of Chemical Physics. https://doi.org/10.1063/5.0012280
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
