| Derivation of Fixed Partial Charges for Amino Acids Accommodating a Specific Water Model and Implicit Polarization. | |
| | |
MedLine Citation:
|
PMID: 23379664 Owner: NLM Status: Publisher |
Abstract/OtherAbstract:
|
We have developed the IPolQ method for fitting non-polarizable point charges to implicitly represent the energy of polarization for systems in pure water. The method involves iterative cycles of molecular dynamics simulations to estimate the water charge density around the solute of interest followed by quantum mechanical calculations at the MP2/cc-pV(T+d)Z level to determine updated solute charges. Lennard-Jones parameters are updated starting from the Amber FF99SB nonbonded parameter set to accommodate the new charge model, guided by the comparisons to experimental hydration free energies (HFEs) of neutral amino acid side chain analogs and assumptions about the computed HFEs for charged side chains. These Lennard-Jones parameter adjustments for side chain analogs are assumed to be transferable to amino acids generally, and new charges for all standard amino acids are then derived in the presence of water modeled by TIP4P-Ew. Overall, the new charges depict substantially more polarized amino acids, particularly in the backbone moieties, than previous Amber charge sets. Efforts to complete a new force field with appropriate torsion parameters for this charge model are underway. The IPolQ method is general, applicable to arbitrary solutes. |
| | |
Authors:
|
David S Cerutti; Julia E Rice; William Swope; David A Case |
Related Documents
:
|
20165424 - Water vapor absorption of carbon dioxide laser radiation. 23153644 - Synthese and characterization of boronic acid functionalized macroporous uniform poly(4... 23181554 - Speciation of la(iii) chloride complexes in water and acetonitrile: a density functiona... 23361354 - Quantification of photocatalytic hydrogen evolution. 15124204 - Drying of poloxamer hydrogel films. 14980764 - Development of pulsatile release tablets with swelling and rupturable layers. |
Publication Detail:
|
Type: JOURNAL ARTICLE Date: 2013-2-5 |
Journal Detail:
|
Title: The journal of physical chemistry. B Volume: - ISSN: 1520-5207 ISO Abbreviation: J Phys Chem B Publication Date: 2013 Feb |
Date Detail:
|
Created Date: 2013-2-5 Completed Date: - Revised Date: - |
Medline Journal Info:
|
Nlm Unique ID: 101157530 Medline TA: J Phys Chem B Country: - |
Other Details:
|
Languages: ENG Pagination: - Citation Subset: - |
Export Citation:
|
APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
|
|
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
Previous Document: Estimating Strain-Specific and Overall Efficacy of Polyvalent Vaccines Against Recurrent Pathogens F...
Next Document: Can Hybrid Solar-Fossil Power Plants mitigate CO2 at Lower Cost than PV or CSP?