Towards the simulation of biomolecules: optimisation of peptide-capped glycine using FFLUX

References

• Rauscher S , Gapsys V , Gajda MJ , et al . Structural ensembles of intrinsically disordered proteins depend strongly on force field: a comparison to experiment. J Chem Theory Comput. 2015;11:5513–5524.10.1021/acs.jctc.5b00736
   PubMed Web of Science ®Google Scholar
• Chapman DE , Steck JK . Nerenberg PS optimizing protein−protein van der waals interactions for the AMBER ff9x/ff12 force field. J Chem Theory Comput. 2014;10:273–281.10.1021/ct400610x
   PubMed Web of Science ®Google Scholar
• Mu Y , Kosov DS , Stock G . Conformational dynamics of trialanine in water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS force fields to NMR and infrared experiments. J Phys Chem B. 2003;107:5064–5073.10.1021/jp022445a
   Web of Science ®Google Scholar
• Piana S , Donchev AG , Robustelli P , et al . Water dispersion interactions strongly influenec simulated structural properties of disordered protein states. J Phys Chem B. 2015;119:5113–5123.10.1021/jp508971m
   PubMedGoogle Scholar
• Vitalini F , Mey AS , Noe F , et al . Dynamic properties of force fields. J Chem Phys. 2015;142:084101.10.1063/1.4909549
   PubMed Web of Science ®Google Scholar
• Gnanakaran S , Garcia AE . Validation of an all-atom protein force field: from dipeptides to larger peptides. J Phys Chem B. 2003;107:12555–12557.10.1021/jp0359079
   Web of Science ®Google Scholar
• Bultinck P , Vanholme R , Popelier PLA , et al . Geerlings P high-speed calculation of AIM charges through the electronegativity equalization method. J Phys Chem A. 2004;108:10359–10366.10.1021/jp046928 l
   Web of Science ®Google Scholar
• Cornell WD , Cieplak P , Bayly CI , et al . A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc. 1995;117:5179–5197.10.1021/ja00124a002
   Web of Science ®Google Scholar
• Joubert L , Popelier PLA . The prediction of energies and geometries of hydrogen bonded DNA base-pairs via a topological electrostatic potential. Phys Chem Chem Phys. 2002;4:4353–4359.10.1039/b204485d
   Web of Science ®Google Scholar
• Cardamone S , Hughes TJ , Popelier PLA . Multipolar electrostatics. Phys Chem Chem Phys. 2014;16:10367–10387.10.1039/c3cp54829e
   PubMed Web of Science ®Google Scholar
• Rafat M , Popelier PLA . A convergent multipole expansion for 1,3 and 1,4 Coulomb interactions. J Chem Phys. 2006;124:144102–144101-144107.
   PubMed Web of Science ®Google Scholar
• Popelier PLA , Kosov DS . Atom-atom partitioning of intramolecular and intermolecular Coulomb energy. J Chem Phys. 2001;114:6539–6547.10.1063/1.1356013
   Web of Science ®Google Scholar
• Solano CJF , Pendás AM , Francisco E , et al . Convergence of the multipole expansion for 1,2 Coulomb interactions: the modified multipole shifting algorithm. J Chem Phys. 2010;132:194110.10.1063/1.3430523
   PubMed Web of Science ®Google Scholar
• Popelier PLA , Stone AJ . Formulae for the first and second derivatives of anisotropic potentials with respect to geometrical parameters. Mol Phys. 1994;82:411–425.
   Web of Science ®Google Scholar
• Blanco MA , Martín Pendás A , Francisco E . Interacting quantum atoms: a correlated energy decomposition scheme based on the quantum theory of atoms in molecules. J Chem Theory Comput. 2005;1:1096–1109.10.1021/ct0501093
   PubMed Web of Science ®Google Scholar
• Popelier PLA . Quantum Chemical Topology. In: Mingos M , editor. The chemical bond – 100 years old and getting stronger. Cham: Springer; 2016. p. 71–117.
   Google Scholar
• Popelier PLA , Aicken FM . Atomic properties of selected biomolecules: Quantum topological atom types of carbon occuring in natural amino acids and derived molecules. J Am Chem Soc. 2003;125:1284–1292.10.1021/ja0284198
   PubMed Web of Science ®Google Scholar
• Bader RFW , Beddall PM . Virial field relationship for molecular charge distributions and the spatial partitioning of molecular properties. J Chem Phys. 1972;56:3320–3329.10.1063/1.1677699
   Web of Science ®Google Scholar
• Bader RFW . Atoms in molecules. A Quantum theory. Oxford: Oxford University Press; 1990.
   Google Scholar
• Popelier PLA . Quantum chemical topology: on bonds and potentials, structure and bonding. In: Wales DJ , editor. Intermolecular forces and clusters. Heidelberg: Springer; 2005. p. 1–56.
   Google Scholar
• Popelier PLA . On Quantum chemical topology. In: Chauvin R , Lepetit C , Alikhani E , Silvi B , editors. Challenges and advances in computational chemistry and physics dedicated to ‘applications of topological methods in molecular chemistry’. Cham: Springer; 2016. p. 23–52.
   Google Scholar
• Stern HA , Rittner F , Berne BJ , et al . Combined fluctuating charge and polarizable dipole models: application to a five-site water potential function. J Chem Phys. 2001;115:2237–2251.10.1063/1.1376165
   Web of Science ®Google Scholar
• Rick SW , Stuart SJ , Berne BJ . Dynamical fluctuating charge force fields: application to liquid water. J Chem Phys. 1994;101:6141–6156.10.1063/1.468398
   Web of Science ®Google Scholar
• Sprik M , Klein ML . A polarizable model for water using distributed charge sites. J Chem Phys. 1988;89:7556–7560.10.1063/1.455722
   Web of Science ®Google Scholar
• Ren P , Ponder JW . Polarizable atomic multipole water model for molecular mechanics simulation. J Phys Chem B. 2003;107:5933.10.1021/jp027815+
   Web of Science ®Google Scholar
• Ponder JW , Wu C , Pande VS , et al . Current status of the AMOEBA polarizable force field. J Phys Chem B. 2010;114:2549–2564.10.1021/jp910674d
   PubMed Web of Science ®Google Scholar
• Piquemal J-P , Chelli R , Procacci P , et al . Key role of the polarization anisotropy of water in modeling classical polarizable force fields. J Phys Chem A. 2007;111:8170–8176.10.1021/jp072687 g
   PubMed Web of Science ®Google Scholar
• Chen W , Gordon MS . The effective fragment potential model for solvation: internal rotation in formamide. J Chem Phys. 1996;105:11081.10.1063/1.472909
   Web of Science ®Google Scholar
• Gordon MS , Slipchenko L , Li H , et al . The effective fragment potential: a general method for predicting intermolecular interactions. Annu Rep Comput Chem. 2007;3:177–193.10.1016/S1574-1400(07)03010-1
   Google Scholar
• Darley MG , Handley CM , Popelier PLA . Beyond point charges: dynamic polarization from neural net predicted multipole moments. J Chem Theory Comput. 2008;4:1435–1448.10.1021/ct800166r
   PubMed Web of Science ®Google Scholar
• Handley CM , Popelier PLA . A dynamically polarizable water potential based on multipole moments trained by machine learning. J Chem Theory Comput. 2009;5:1474–1489.10.1021/ct800468 h
   PubMed Web of Science ®Google Scholar
• Cressie N . Statistics for spatial data. New York (NY): Wiley; 1993.
   Google Scholar
• In Het Panhuis, M , Popelier, PLA , Munn, RW , et al . Distributed polarizability of the water dimer: charge transfer along the hydrogen bond. J Chem Phys. 2001;114:7951–7961.
   Web of Science ®Google Scholar
• Fletcher TL , Kandathil SM , Popelier PLA . The prediction of atomic kinetic energies from coordinates of surrounding atoms using kriging machine learning. Theor Chem Acc. 2014;133(1499):1491–1410.
   Google Scholar
• Maxwell P , di Pasquale N , Cardamone S , et al . The prediction of topologically partitioned intra-atomic and inter-atomic energies by the machine learning method kriging. Theoret Chem Acc. 2016;135:L47.10.1007/s00214-016-1951-4
   Web of Science ®Google Scholar
• McDonagh JL , da Silva A , Vincent MA , et al . Machine learning of dynamic electron correlation energies from topological atoms. J Chem Theor Comput. 2018;14:216–224. doi:10.1021/acs.jctc.7b01157.
   PubMed Web of Science ®Google Scholar
• Maxwell P , Martín Pendás A , Popelier PLA . Extension of the interacting quantum atoms (IQA) approach to B3LYP level density functional theory. PhysChemChemPhys. 2016;18:20986–21000.
   Google Scholar
• Popelier PLA QCTFF . On the construction of a novel protein force field. Int J Quant Chem. 2015;115:1005–1011.
   Web of Science ®Google Scholar
• Jensen F . Introduction of computational chemistry. 2nd ed. Chichester: Wiley; 2007.
   Google Scholar
• Vanommeslaeghe K , Hatcher A , Acharya C , et al . CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM All-Atom Additive Biological Force Fields. J Comp Chem. 2010;31:671–690.
   PubMed Web of Science ®Google Scholar
• van Duin ACT , Dasgupta S , Lorant F . Goddard WA ReaxFF: a reactive force field for hydrocarbons. J Phys Chem A. 2001;105:9396–9409.10.1021/jp004368u
   Web of Science ®Google Scholar
• Mills MJL , Popelier PLA . Electrostatic forces: formulae for the first derivatives of a polarisable, anisotropic electrostatic potential energy function based on machine learning. J Chem Theory Comput. 2014;10:3840–3856.10.1021/ct500565 g
   PubMed Web of Science ®Google Scholar
• Zielinski F , Maxwell PI , Fletcher TL , et al . Geometry optimization with machine trained topological atoms. Sci Rep. 2017;7:1096.10.1038/s41598-017-12600-3
   PubMed Web of Science ®Google Scholar
• Popelier PLA . Molecular simulation by knowledgeable Quantum atoms. Phys Scr. 2016;91:033007.
   Web of Science ®Google Scholar
• Bertoni C , Gordon MS . Analytic gradients for the effective fragment molecular orbital method. J Chem Theory Comput. 2016;12:4743–4767.10.1021/acs.jctc.6b00337
   PubMed Web of Science ®Google Scholar
• Stone AJ . Theory of intermolecular forces. 1st ed. Oxford: Clarendon Press; 1996.
   Google Scholar
• Jones DR , Schonlau M , Welch WJ . Efficient global optimization of expensive black-box functions. J Global Optim. 1998;13:455–492.10.1023/A:1008306431147
   Web of Science ®Google Scholar
• Kandathil SM , Fletcher TL , Yuan Y , et al . Accuracy and tractability of a kriging model of intramolecular polarizable multipolar electrostatics and its application to histidine. J Comput Chem. 2013;34:1850–1861.10.1002/jcc.23333
   PubMed Web of Science ®Google Scholar
• Yuan Y , Mills MJL , Popelier PLA , et al . Comprehensive analysis of energy minima of the 20 natural amino acids. J Phys Chem A. 2014;118:7876–7891.10.1021/jp503460 m
   PubMed Web of Science ®Google Scholar
• Jensen F . Polarization consistent basis sets. III. The importance of diffuse functions. J Chem Phys. 2002;117:9234–9240.10.1063/1.1515484
   Web of Science ®Google Scholar
• Zupan J , Gasteiger J . Neural networks in chemistry and drug design. 2nd ed. Weinheim: VCH-Wiley; 1999.
   Google Scholar
• AIMAll, Keith TA . TK Gristmill Software. Overland Park, KS; 2016.
   Google Scholar
• Di Pasquale N , Bane M , Davie SJ , et al . FEREBUS: highly parallelized engine for kriging training. J Comput Chem. 2016;37:2606–2616.10.1002/jcc.v37.29
   PubMed Web of Science ®Google Scholar
• Mills MJL , Popelier PLA . Polarisable multipolar electrostatics from the machine learning method Kriging: an application to alanine. Theoret Chem Acc. 2012;131:1137–123911153.10.1007/s00214-012-1137-7
   Web of Science ®Google Scholar
• Todorov IT , Smith W , Trachenko K , et al . DL_POLY_3: new dimensions in molecular dynamics simulations via massive parallelism. J Mater Chem. 2006;16:1911–1918.10.1039/b517931a
   Web of Science ®Google Scholar
• Popelier PLA , Bader RFW . Effect of twisting a polypeptide on its geometry and electron distribution. J Phys Chem. 1994;98:4473–4481.10.1021/j100067a040
   Web of Science ®Google Scholar
• Rafat M , Devereux M , Popelier PLA . Rendering of quantum topological atoms and bonds. J Mol Graph Model. 2005;24:111–120.10.1016/j.jmgm.2005.05.004
   PubMed Web of Science ®Google Scholar