The Force Field Toolkit (fftk)
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1 Parameterizing Small Molecules Using: The Force Field Toolkit (fftk) Christopher G. Mayne, Emad Tajkhorshid Beckman Institute for Advanced Science and Technology University of Illinois, Urbana-Champaign Klaus Schulten University of Illinois, Urbana-Champaign James C. Gumbart, Anna Pavlova Georgia Institute of Technology NIH Hands n Workshop Atlanta November 5th, 2014
2 MD Simulations of Biological Systems Molecular Mechanics Force Fields U = Ubonds + Uangles + Udihedrals + UvdW + Ucoulombic bonded non-bonded The CHARMM Force Field U = Σ k bond - ) i (ri r0 2 + Σ ( θ - ) ki angle i 2 + θ0 bonds angles Σ [1 + cos( + )] ki dihedral niɸi δi dihedrals + Σ i Σ j i 4 ij( σ ij rij ) 12 ( σij ) 6 rij - + ΣΣ qiqj i j i rij
3 MD Simulations of Biological Systems Molecular Mechanics Force Fields U = Ubonds + Uangles + Udihedrals + UvdW + Ucoulombic bonded non-bonded The CHARMM Force Field U = Σ k bond - ) i (ri r0 2 + Σ ( θ - ) ki angle i 2 + θ0 bonds angles Σ [1 + cos( + )] ki dihedral niɸi δi dihedrals + Σ i Σ j i 4 ij( σ ij rij ) 12 ( σij ) 6 rij - + ΣΣ qiqj i j i rij
4 Parameter Transferability In Biopolymers Parameter set describes molecular behavior in varied chemical (connectivity) and spatial (conformation) contexts Peptides and Proteins Nucleic Acids H N Me S Me H H N N N N N H H H Me Me NH 2 H H 2 N N N N N P N NH 2 N P HN N Me P N N N NH NH 2 Key Features: R limited set of isolated building blocks repetitive backbone unit
5 Parameterization as an Impasse H N H non-standard or engineered amino acids CH H 2 N CH HN small molecule ligands N HN N N Me Me N Me S H Me N S N Imatinib (Gleevec) Tiotropium (Spiriva) cofactors metal centers HS N H N H Me H Me P P N N NH 2 N N H 2 N S Fe S NH 2 Coenzyme A H P S NH 2 S H 2 N
6 General Parameterization Workflow PSF/PDB System Preparation Charges Bonds & Angles PAR File Dihedrals / Torsions
7 CGenFF Parameterization Workflow PSF/PDB Find Missing Parameters Geometry ptimization (QM) Water Interaction En. (QM) Charge ptimization Hessian Calculation (QM) Bond & Angle ptimization PAR File Torsion Scan (QM) Torsion ptimization K. Vanommeslaeghe et al., J. Comput. Chem. 2010, 31,
8 CGenFF Parameterization Workflow PSF/PDB PAR File Find Missing Parameters Geometry ptimization (QM) Water Interaction En. (QM) Charge ptimization Hessian Calculation (QM) Bond & Angle ptimization Torsion Scan (QM) Torsion ptimization build init PAR update PDB update PSF update PAR update PAR Calculation Action K. Vanommeslaeghe et al., J. Comput. Chem. 2010, 31,
9 CGenFF Parameterization Workflow PSF/PDB PAR File Find Missing Parameters Geometry ptimization (QM) Water Interaction En. (QM) Charge ptimization Hessian Calculation (QM) Bond & Angle ptimization Torsion Scan (QM) Torsion ptimization build init PAR update PDB update PSF update PAR update PAR Calculation Action C.G. Mayne et al., J. Comput. Chem. 2013, 34,
10 fftk Interface
11 fftk Interface
12 fftk Interface tasks organized under tabs
13 fftk Interface standard file dialogs action buttons action menus
14 Functionality Provided by fftk Setup & Perform Multi-dimensional ptimizations Core Functions Abstraction of Gaussian I/ (QM) Assess Performance of Parameters by Visualizing ptimization Data Support Functions Auto-detect Water Interaction Sites Auto-detect Charge Groups Auto-detect Non-redundant Torsions Build & Update Parameter Files Browse Existing Parameter Sets Write Updated Charges to PSF Reset pt. Input from utput Visualize Target Data in VMD Create Graphic bjects in VMD Label Atoms in VMD Read Input Parameters from File Read/Write Data From pt. Logs Export Plot Data to File Monitor ptimization Progress
15 fftk Exemplified by Charge ptimization PSF/PDB PAR File Find Missing Parameters Geometry ptimization (QM) Water Interaction En. (QM) Charge ptimization Hessian Calculation (QM) Bond & Angle ptimization Torsion Scan (QM) Torsion ptimization build init PAR update PDB update PSF update PAR update PAR Calculation Action
16 fftk Exemplified by Charge ptimization PSF/PDB PAR File Find Missing Parameters Geometry ptimization (QM) Water Interaction En. (QM) Charge ptimization Hessian Calculation (QM) Bond & Angle ptimization Torsion Scan (QM) Torsion ptimization build init PAR update PDB update PSF update PAR update PAR Calculation Action
17 Generating Charge ptimization Target Data Load QM optimized geometry Auto-detect interaction sites Genera pyrrolidine fftk GUI VMD main window
18 Generating Charge ptimization Target Data geometry Auto-detect interaction sites Generate Gaussian Input Files Run Q fftk GUI VMD main window
19 Generating Charge ptimization Target Data geometry Auto-detect interaction sites Generate Gaussian Input Files Run Q fftk GUI Donor VMD main window Acceptor
20 Generating Charge ptimization Target Data n sites Generate Gaussian Input Files Run QM Inspect water optimization Compute water position ptimize distance & rotation fftk GUI
21 Generating Charge ptimization Target Data Run QM Inspect water optimization Visually assess QM-optimized water position(s) fftk GUI
22 Generating Charge ptimization Target Data Run QM Inspect water optimization Visually assess QM-optimized water position(s) fftk GUI
23 Charge ptimization Setup ptimization Load QM Target Data Prepare ptimization ptimizer: Assign Charges Compute UMM, dmm, µmm Compute bjective Function Return ptimized Charges Analyze Performance bjective Function Σ wat. int. Σ wat. int. f(u MM -U QM ) + f(d MM -d QM ) + f(μ MM -μ QM ) Write Charges to PSF
24 Assessing MM Water-Interaction Profiles 10 8 Initial Charges Intermediate Charges Final ptimized Charges Literature Charges U MM-QM (kcal/mol) d MM-QM (Å)
25 Sampling MM Water-Interaction Profiles Mode: Simulated Annealing 6 5 H N H N H H N 4000 H 3 H 2 H ΔdMM-QM (Å) Iteration ΔUMM-QM (kcal/mol) 4 H N 4500
26 Plotting Charge ptimization Data
27 Plotting Charge ptimization Data
28 Plotting Charge ptimization Data
29 Plotting Charge ptimization Data
30 Plotting Charge ptimization Data export data ΔE from Target (kcal/mol) ptimization Iteration
31 Parameterization of Erythromycin macrolides - antibiotics that prevent peptide synthesis in bacterial ribosomes small subunit PTC PET large subunit nascent peptide macrolide Divided into four parts
32 Parameterization of Erythromycin macrolides - antibiotics that prevent peptide synthesis in bacterial ribosomes small subunit PTC PET large subunit nascent peptide macrolide Divided into four parts
33 Parameterization of Erythromycin macrolides - antibiotics that prevent peptide synthesis in bacterial ribosomes small subunit PTC PET large subunit nascent peptide macrolide Divided into four parts
34 Parameterization of Erythromycin macrolides - antibiotics that prevent peptide synthesis in bacterial ribosomes small subunit PTC PET large subunit nascent peptide macrolide Divided into four parts
35 Parameterization of Erythromycin macrolides - antibiotics that prevent peptide synthesis in bacterial ribosomes small subunit PTC PET large subunit nascent peptide macrolide Divided into four parts
36 Parameterization of Erythromycin macrolides - antibiotics that prevent peptide synthesis in bacterial ribosomes small subunit PTC PET large subunit nascent peptide macrolide Divided into four parts
37 Parameterization of Erythromycin macrolides - antibiotics that prevent peptide synthesis in bacterial ribosomes small subunit PTC PET large subunit nascent peptide macrolide Divided into four parts
38 Fitting of Partial Charges CHARMM partial charges are derived from interactions with water! Calculated for each atom that is fitted
39 Fitting of Partial Charges CHARMM partial charges are derived from interactions with water! Calculated for each atom that is fitted
40 Fitting of Partial Charges CHARMM partial charges are derived from interactions with water! Calculated for each atom that is fitted Loaded into FFTK
41 Accuracy of Fitting: Charges Partial charges for polar atoms Desosamine charges fitted for red atoms Charge CGenFF FFTK H1 H' FFTK can be used to get better agreement with QM data
42 Accuracy of Fitting: Charges Interaction Partial energies charges with for water polar for atoms polar atoms Desosamine charges fitted for red atoms E (kcal/mol) Charge CGenFF FFTK CGenFF FFTK QME H1 H' H1 H' FFTK can be used to get better agreement with QM data
43 Fitting of Partial Charges! ptimization of water interactions can be difficult for sterically hindered groups! ur self consistent iterative charge optimization scheme! Desosamine) Simpli&ied)Desosamine) H H 3 C N CH 3 CH 3 H CH 3 H H 3 C N H CH 3 H
44 Fitting of Partial Charges! ptimization of water interactions can be difficult for sterically hindered groups! ur self consistent iterative charge optimization scheme! Desosamine) Simpli&ied)Desosamine) H H 3 C N CH 3 CH 3 H CH 3 H H 3 C N H CH 3 H
45 Fitting of Partial Charges! ptimization of water interactions can be difficult for sterically hindered groups! ur self consistent iterative charge optimization scheme! Desosamine) Simpli&ied)Desosamine) H H 3 C N CH 3 CH 3 H CH 3 H H 3 C N H CH 3 H
46 An Alternative to Water Interactions for Charges RESP fitting of charges! Based electrostatic potential!!! Much easier to implement! Tests on compatibility with CHARMM in progress
47 An Alternative to Water Interactions for Charges RESP fitting of charges! Based electrostatic potential!!! Much easier to implement! Tests on compatibility with CHARMM in progress
48 Fitting of Bonds and Angles
49 Fitting of Bonds and Angles input Hessian file
50 Fitting of Bonds and Angles input Hessian file btained! force constants! and values
51 Fitting of Dihedrals K (1 + cos(n ))
52 Fitting of Dihedrals Feed in the dihedral scans K (1 + cos(n ))
53 Fitting of Dihedrals Select multiplicity and phase settings K (1 + cos(n ))
54 Fitting of Dihedrals Select multiplicity and phase settings multiplicity phase multiplicity phase K (1 + cos(n ))
55 Fitting of Dihedrals First fit is not great but better than the starting fit QM PES: black! First fit: blue! Starting fit: red!
56 Fitting of Dihedrals After 7 iterations the fit is much better First fit is not great but better than the starting fit QM PES: black! First fit: blue! Starting fit: red!
57 Two Approaches to Fitting the Dihedrals Several multiplicities! and free phase ne multiplicity and! locked phase Pro: very good fit of QM PES! Cons: possible incorrect behavior! multiple sets of force constants Pros: limits incorrect behavior,! sets of force constants! Con: fit to QM PES not always! possible In practice a tradeoff is needed!
58 Example of verfitting imidazole-pyrridine moiety of antibiotic telithromycin
59 Example of verfitting imidazole-pyrridine moiety of antibiotic telithromycin E (kcal/mol) multiplicities, free phase Dihedral Fit QM PES MM Fit Configuration
60 Example of verfitting imidazole-pyrridine moiety of antibiotic telithromycin
61 Example of verfitting imidazole-pyrridine moiety of antibiotic telithromycin
62 Example of verfitting imidazole-pyrridine moiety of antibiotic telithromycin Using too many dihedral multiplicities can leads to distortion of a planar molecule!
63 Example of verfitting imidazole-pyrridine moiety of antibiotic telithromycin
64 Example of verfitting imidazole-pyrridine moiety of antibiotic telithromycin planar dihedrals have multiplicity 2 and phase 180
65 Example of verfitting imidazole-pyrridine moiety of antibiotic telithromycin planar dihedrals have multiplicity 2 and phase 180 E (kcal/mol) Dihedral Fitting QM PES MM Fit Configuration The fit looks even better!
66 Example of verfitting imidazole-pyrridine moiety of antibiotic telithromycin planar dihedrals have multiplicity 2 and phase 180
67 Example of verfitting imidazole-pyrridine moiety of antibiotic telithromycin planar dihedrals have multiplicity 2 and phase 180 Planarity is maintained!
68 Example of verfitting imidazole-pyrridine moiety of antibiotic telithromycin Problems persist eclipsed conformation of the alkane part
69 Example of verfitting imidazole-pyrridine moiety of antibiotic telithromycin Problems persist eclipsed conformation of the alkane part Restraining phase of CH dihedrals to 0 prevents eclipsed confirmations
70 How to know what terms to include?
71 fftk: Find Missing Parameters Geometry ptimization (QM) Water Interaction En. (QM) Charge ptimization Hessian Calculation (QM) Bond & Angle ptimization Torsion Scan (QM) Torsion ptimization Conclusions - Simplifies the parameterization workflow - ffers opportunity for extensive customization - Provides analytical tools to assess parameter performance
72 Future Directions Investigate forcefield performance Support additional force fields (e.g. AMBER) Improve optimization speed Expand analysis tools Support multiple QM packages
73 fftk Mayne et al.; J. Comp. Chem. 2013, 34, pp fftk is available as a VMD Plugin (1.9.1 or newer) Journal of Volume 34 Issues Included in this print edition: Issue 31 (December 5, 2013) Issue 32 (December 15, 2013) CMPUTATINAL rganic CHEMISTRY Inorganic Physical Biological Materials Research in Systems Neuroscience Editors: Charles L. Brooks III Masahiro Ehara Gernot Frenking Peter R. Schreiner Questions?
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