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Title: Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15

Authors:
ORCiD logo; ; ; ; ORCiD logo; ; ORCiD logo; ORCiD logo;
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1368571
DOE Contract Number:
AC02-76SF00515; P30CA008747; U19 AI109662; I8-A8-058; R01 GM062868; ACI-1450179; CHE-1363320
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry; Journal Volume: 121; Journal Issue: 16
Country of Publication:
United States
Language:
English

Citation Formats

Wang, Lee-Ping, McKiernan, Keri A., Gomes, Joseph, Beauchamp, Kyle A., Head-Gordon, Teresa, Rice, Julia E., Swope, William C., Martínez, Todd J., and Pande, Vijay S. Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15. United States: N. p., 2017. Web. doi:10.1021/acs.jpcb.7b02320.
Wang, Lee-Ping, McKiernan, Keri A., Gomes, Joseph, Beauchamp, Kyle A., Head-Gordon, Teresa, Rice, Julia E., Swope, William C., Martínez, Todd J., & Pande, Vijay S. Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15. United States. doi:10.1021/acs.jpcb.7b02320.
Wang, Lee-Ping, McKiernan, Keri A., Gomes, Joseph, Beauchamp, Kyle A., Head-Gordon, Teresa, Rice, Julia E., Swope, William C., Martínez, Todd J., and Pande, Vijay S. Thu . "Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15". United States. doi:10.1021/acs.jpcb.7b02320.
@article{osti_1368571,
title = {Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15},
author = {Wang, Lee-Ping and McKiernan, Keri A. and Gomes, Joseph and Beauchamp, Kyle A. and Head-Gordon, Teresa and Rice, Julia E. and Swope, William C. and Martínez, Todd J. and Pande, Vijay S.},
abstractNote = {},
doi = {10.1021/acs.jpcb.7b02320},
journal = {Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry},
number = 16,
volume = 121,
place = {United States},
year = {Thu Apr 06 00:00:00 EDT 2017},
month = {Thu Apr 06 00:00:00 EDT 2017}
}
  • Here we report that proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find themore » optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.« less
  • Nanoparticles of Ni{sub 1−x}Zn{sub x}O and Ni{sub 1−x}Zn{sub x}O/ZnO, which can be good candidates for selective gas sensors, were successfully obtained via a two-step synthetic route, in which the nickel zinc malonate precursor was first synthesized by co-precipitation from an aqueous solution, followed by pyrolysis in air at a relatively low temperature (~500 °C). The precursor was characterized by ICP-AES, FTIR and TG and the results indicate the molecular structure of the precursor to be compatible with Ni{sub 1−x}Zn{sub x}(OOCCH{sub 2}COO)·2H{sub 2}O. The decomposition product, characterized using various techniques (FTIR, XRD, ToF-SIMS, SEM, TEM and XPS), was established to bemore » a doped nickel oxide (Ni{sub 1−x}Zn{sub x}O for 0.01≤x≤0.1) and a composite material (Ni{sub 1−x}Zn{sub x}O/ZnO for 0.2≤x≤0.5). To elucidate the form in which the Zn is present in the NiO structure, three analytical techniques were employed: ToF-SIMS, XRD and XPS. While ToF SIMS provided a direct evidence of the presence of Zn in the NiO crystal structure, XRD showed that Zn actually substitutes Ni in the structure and XPS is a bit more specific by indicating that the Zn is present in the form of Zn{sup 2+} ions. - Highlights: • Coprecipitation synthesis of nickel zinc malonate single bath precursor was achieved. • The as synthesized precursors are an homogeneous mixture of nickel and zinc malonate. • XRD, ToF-SIMS, XPS, SEM and TEM was used to characterized decomposition products. • Ni{sub 1−x}Zn{sub x}O nanoparticles (0.01≤x≤0.1) formed after pyrolysis (~500 °C) of precursor. • Ni{sub 1−x}Zn{sub x}O/ZnO nanocomposite (0.2≤x≤0.5) formed after pyrolysis at 500 °C of precursor.« less
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