merged my edits from an old master and fixed reference probs

Author: hmayes

paper/basic_training.bib

@@ -174,18 +174,21 @@ @article{amber15FB
 }
 
 @article{mackerell2004CMAP,
-author = {Mackerell Alexander D. and Feig Michael and Brooks Charles L.},
-title = {Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations},
-journal = {Journal of Computational Chemistry},
-volume = {25},
-number = {11},
-pages = {1400-1415},
-keywords = {ab initio, CMAP, molecular dynamics, dihedral angles, empirical force field, molecular mechanics},
+author = {{Mackerell, Jr.}, Alexander D. and Feig, Michael and {Brooks, III}, Charles L.},
 doi = {10.1002/jcc.20065},
+journal = {J. Comput. Chem.},
+keywords = {ab initio,cmap,dihedral angles,empirical force field,molecular dynamics,molecular mechanics},
+number = {11},
+pages = {1400--1415},
+title = {{Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations}},
 url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20065},
-eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20065}
+volume = {25},
+year = {2004}
 }
 
+
+
+
 @article{perez2015,
 author = {Perez, Alberto and MacCallum, Justin L. and Brini, Emiliano and Simmerling, Carlos and Dill, Ken A.},
 doi = {10.1021/acs.jctc.5b00662},
@@ -290,7 +293,7 @@ @article{Mishra2017
 @article{Lopes2009,
 archivePrefix = {arXiv},
 arxivId = {NIHMS150003},
-author = {Lopes, Pedro E.M. and Roux, Benoit and MacKerell, Alexander D.},
+author = {Lopes, Pedro E.M. and Roux, Benoit and {Mackerell, Jr.}, Alexander D.},
 doi = {10.1007/s00214-009-0617-x},
 eprint = {NIHMS150003},
 file = {:Users/jacobmonroe/Documents/Papers{\_}Library/Best{\_}Practices/Lopes2009{\_}Polarizable{\_}models{\_}review.pdf:pdf},
@@ -370,7 +373,7 @@ @article{Grossfield:2009:AnnuRepComputChem
   pmcid = {PMC2865156}
 }
 
-@article{Zuckerman:2011:Annu.Rev.Biophys.,
+@article{Zuckerman:2011:AnnuRevBiophys,
   title = {Equilibrium {{Sampling}} in {{Biomolecular Simulations}}},
   volume = {40},
   doi = {10.1146/annurev-biophys-042910-155255},
@@ -409,7 +412,7 @@ @misc{Zuckerman:2015:StatisticalBiophysicsBlog
   file = {/Users/dmobley/Zotero/storage/KAQSYA4R/statisticalbiophysicsblog.org.html}
 }
 
-@article{Zuckerman:2017:Annu.Rev.Biophys.,
+@article{Zuckerman:2017:AnnuRevBiophys,
   title = {Weighted {{Ensemble Simulation}}: {{Review}} of {{Methodology}}, {{Applications}}, and {{Software}}},
   volume = {46},
   shorttitle = {Weighted {{Ensemble Simulation}}},
@@ -436,7 +439,7 @@ @book{Zuckerman:2010:
   file = {/Users/dmobley/Zotero/storage/5GL7B76J/9781420073782.html}
 }
 
-@article{Ponder:2010:J.Phys.Chem.B,
+@article{Ponder:2010:JPhysChemB,
   title = {Current {{Status}} of the {{AMOEBA Polarizable Force Field}}},
   volume = {114},
   issn = {1520-6106},
@@ -449,21 +452,21 @@ @article{Ponder:2010:J.Phys.Chem.B
   pages = {2549-2564},
 }
 
-@article{Lemkul:2016:Chem.Rev.,
+@article{Lemkul:2016:ChemRev,
   title = {An {{Empirical Polarizable Force Field Based}} on the {{Classical Drude Oscillator Model}}: {{Development History}} and {{Recent Applications}}},
   volume = {116},
   issn = {0009-2665},
   shorttitle = {An {{Empirical Polarizable Force Field Based}} on the {{Classical Drude Oscillator Model}}},
   doi = {10.1021/acs.chemrev.5b00505},
   number = {9},
   journal = {Chem. Rev.},
-  author = {Lemkul, Justin A. and Huang, Jing and Roux, Beno\^it and MacKerell, Alexander D.},
+  author = {Lemkul, Justin A. and Huang, Jing and Roux, Beno\^it and {Mackerell, Jr.}, Alexander D.},
   month = may,
   year = {2016},
   pages = {4983-5013},
 }
 
-@article{York:1993:J.Chem.Phys.,
+@article{York:1993:JChemPhys,
   title = {The Effect of Long-range Electrostatic Interactions in Simulations of Macromolecular Crystals: {{A}} Comparison of the {{Ewald}} and Truncated List Methods},
   volume = {99},
   issn = {0021-9606, 1089-7690},
@@ -478,7 +481,7 @@ @article{York:1993:J.Chem.Phys.
   pages = {8345-8348},
 }
 
-@article{Darden:1993:J.Chem.Phys.,
+@article{Darden:1993:JChemPhys,
   title = {Particle Mesh {{Ewald}}: {{An N}} Log( {{N}} ) Method for {{Ewald}} Sums in Large Systems},
   volume = {98},
   issn = {0021-9606, 1089-7690},
@@ -493,7 +496,7 @@ @article{Darden:1993:J.Chem.Phys.
   pages = {10089-10092},
 }
 
-@article{Sagui:1999:Annu.Rev.Biophys.Biomol.Struct.,
+@article{Sagui:1999:AnnuRevBiophysBiomolStruct,
   title = {{{MOLECULAR DYNAMICS SIMULATIONS OF BIOMOLECULES}}: {{Long}}-{{Range Electrostatic Effects}}},
   volume = {28},
   shorttitle = {{{MOLECULAR DYNAMICS SIMULATIONS OF BIOMOLECULES}}},
@@ -506,7 +509,7 @@ @article{Sagui:1999:Annu.Rev.Biophys.Biomol.Struct.
   pmid = {10410799}
 }
 
-@article{Cisneros:2014:Chem.Rev.,
+@article{Cisneros:2014:ChemRev,
   title = {Classical {{Electrostatics}} for {{Biomolecular Simulations}}},
   volume = {114},
   issn = {0009-2665, 1520-6890},
@@ -520,7 +523,7 @@ @article{Cisneros:2014:Chem.Rev.
   pages = {779-814},
 }
 
-@article{Basconi:2013:J.Chem.TheoryComput.,
+@article{Basconi:2013:JChemTheoryComput,
   title = {Effects of {{Temperature Control Algorithms}} on {{Transport Properties}} and {{Kinetics}} in {{Molecular Dynamics Simulations}}},
   volume = {9},
   issn = {1549-9618},
@@ -533,7 +536,7 @@ @article{Basconi:2013:J.Chem.TheoryComput.
   pages = {2887-2899},
 }
 
-@article{Shirts:2013:J.Chem.TheoryComput.,
+@article{Shirts:2013:JChemTheoryComput,
   title = {Simple {{Quantitative Tests}} to {{Validate Sampling}} from {{Thermodynamic Ensembles}}},
   volume = {9},
   issn = {1549-9618},
@@ -631,7 +634,7 @@ @article{Onufriev2018
 year = {2018}
 }
 
-@article{Dupradeau:2010:Phys.Chem.Chem.Phys.,
+@article{Dupradeau:2010:PhysChemChemPhys,
   title = {The {{R}}.{{E}}.{{D}}. Tools: Advances in {{RESP}} and {{ESP}} Charge Derivation and Force Field Library Building},
   volume = {12},
   issn = {1463-9084},
@@ -887,7 +890,7 @@ @article{Shirts:2007:JPhysChemB
   pages = {13052-13063},
 }
 
-@article{Chen:2014:Mol.Simul.,
+@article{Chen:2014:MolSimul,
   title = {Recent Development and Application of Constant {{pH}} Molecular Dynamics},
   volume = {40},
   issn = {0892-7022},