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Running AMBER Running AMBER suite programs: Ini4aliza4on: source /home/ei250498/PROGRAMS/modules/amber.sh antechamber XLEaP: xleap –f /home/ei250498/PROGRAMS/src/amber11/dat/leap/cmd/leaprc.ff99SB & loadamberprep acetone.resp.prep loadamberparams /home/ei250498/PROGRAMS/src/amber11/dat/leap/parm/gaff.dat loadamberparams /home/ei250498/TUTORIAL/ACETONE/5-‐XLEAP/acetone.frcmod saveamberparm ACET acetone.top acetone.rst solvatebox ACET TIP3PBOX 14 saveamberparm ACET acetone_solv.top acetone_solv.rst
Antechamber – rapid genera4on of topology files for use with the AMBER simula4on programs • Automa4cally iden4fy bond and atom types • Judge atomic equivalence • Generate residue topology files • Find missing force field parameters and supply reasonable sugges4ons – antechamber executes the following programs (all provided with AmberTools): • divcon, atomtype, am1bcc, bondtype, espgen, respgen, prepgen -‐i -‐fi -‐c -‐o -‐nc -‐m -‐fo -‐rn inpuƒile name format inpuƒile [gout=Gaussian output, gzmat, pdb, mdl, ...] resp = use RESP charge model [Mulliken, bcc, ...] output filename net molecular charge (int) mul4plicity (2S+1), default=1 output file format [prepi = AMBER Prep (int)] residue name (unit), if not available in the input file (default: mol)
Page 1 and 2: From Molecular to Con/nuum Phys
Page 3 and 4: Car-Parinello / Molecular Mechanics
Page 5 and 6: Potential Energy Surfaces • Geome
Page 7 and 8: Molecular Dipole Moments • Molecu
Page 9 and 10: Quantum Mechanical Dipole Moments
Page 11 and 12: Molecular Dipole Moments Alignment
Page 13 and 14: Dipole Moment Of Acetone • Proced
Page 15 and 16: Internal Coordinates Bond lengths
Page 17 and 18: CPMD Input • General - Sec4ons:
Page 19 and 20: CPMD Input • &SYSTEM … &END
Page 21 and 22: Choosing the Plane Wave Cutoff •
Page 23 and 24: CPMD Input • &ATOMS … &END (
Page 25 and 26: CPMD Output • Header - Date whe
Page 27 and 28: CPMD Output • Atoms: coordinates
Page 29 and 30: CPMD Output • Distribu4on among
Page 31 and 32: CPMD Output • Ini4al guess for
Page 33 and 34: CPMD Output • Geometry op4miza4o
Page 39 and 40: Force field: Bonded terms (not used
Page 41 and 42: Acetone in Water: Electrostatic Int
Page 45 and 46: Running Gaussian 1. Set the envir
Page 49 and 50: Antechamber - automates the proce
Page 51: Antechamber - automates the proce
Page 55 and 56: Acetone: Pre-Equilibration • Clas
Page 57 and 58: Acetone: Topology File %VERSION VER
Page 59 and 60: Acetone in Water: Water Box - Autom
Page 61 and 62: Water Models - Water models diffe
Page 63 and 64: Water Models http://www.lsbu.ac.uk/
Page 65 and 66: Sander: Pre-Equilibration • 1. C
Page 67 and 68: Sander: Usage
Page 69 and 70: Sander: 1. Restrained Minimization
Page 71 and 72: Sander: 2. Unrestrained Minimizatio
Page 73 and 74: Sander: 3. MD at 300 K (NVT ensembl
Page 75 and 76: Vibrational Motions • High-‐f
Page 77 and 78: Statistical Thermodynamics • Cano
Page 79 and 80: Sander: 3. MD at 300 K (Heating)
Page 81 and 82: Sander: 4. MD at 300 K / 1 atm (NPT
Page 83 and 84: Analysis and Processing: Reimaging
Page 85 and 86: Ab initio MD • Born-‐Oppenhei
Page 87 and 88: Ab initio MD: CPMD • Adiaba4c se
Page 89 and 90: Ab initio MD: CPMD • How to con
Page 91 and 92: QM/MM: Production • Controlling
Page 93 and 94: QM/MM • Combina4on of accuracy
Page 95 and 96: QM/MM: Electrostatic interaction
Page 97 and 98: QM/MM: CPMD/GROMOS • Hamiltonian
Page 99 and 100: QM/MM: CPMD/GROMOS • Long-‐ra
Page 101 and 102: QM/MM: CPMD/GROMOS • Forces •
Page 103 and 104:
QM/MM Input: Classical Input File T
Page 105 and 106:
QM/MM Input: Classical Topology Fil
Page 107 and 108:
QM/MM Input: Classical Topology Fil
Page 109 and 110:
QM/MM Input: QM Part - CPMD Input &
Page 111 and 112:
QM/MM Input: QM Part - CPMD Input &
Page 113 and 114:
QM/MM Output: Simulated Annealing
Page 115 and 116:
Car-Parrinello Lagrangian L = T −
Page 117 and 118:
QM/MM Output: Simulated Annealing
Page 119 and 120:
QM/MM Output: Simulated Annealing 9
Page 121 and 122:
QM/MM: Test - Result: temperature
Page 123 and 124:
QM/MM: Heating - Hea4ng of the s
Page 125 and 126:
QM/MM: Production • QM/MM-‐CP
Page 127 and 128:
QM/MM: Dipole Moment Calculation -
Page 129 and 130:
QM/MM: Dipole Moment Calculation
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