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Calculation Times Required for Single-Point Calculations and Geometry Optimizations in the Side Chain Rotamer Modeling Program The auto-rotamer search function of the Side Chain Rotamer Modeling program automatically generates an output log file of the calculation conditions and results. The following results referred the Total Time in this log file.
Used System CPU: Intel Pentium4 3.20EGHz (FSB 800 MHz; L2 1MB) Memory: PC3200 (Dual Channel) CL3 4GB Chip Set: Intel I875P SCSI: Ultra320 HDD: Ultra320 36GB OS: Microsoft Windows XP Professional SP2 HyperChem: version 7.5.1
Rotation Angles: Gamma, 60.0; Delta, 60.0; Epsilon, 60.0; Zeta, 60.0 (deg.) Off Redispaly Force Field: AMBER94 Dielectric: Distance Dependent; Scale Factor, 1.0 1-4 Scale Factors: Electrostatic, 0.833; van der Waals, 0.5 Cutoffs: None Use All Atom Conditions Single Point Calculations or Geometry Optimization Polak-Ribiere RMS Gradient: 1.0, Maximum Cycles: 100
Other Bench Mark Tests Test 1: bovine Rhodopsin 1HZX (PDB Format) Total Molecules: 40 Total Atoms: 10,761 Total Proteins: 2 Waters: 12 Other Molecules: 26 Total Residues in Proteins: 659 Total Leucines in Proteins: 55 Total Lone Pairs in Proteins: 102 Total Atoms in Proteins: 10,505
Geometry Correction Leucines: < 1 s Lone Pairs: < 1 s
Estimation of Hydrogen Atoms in Water Estimation (contain redraw): < 22 s
Homology Modeling Alignment: < 1 s Modeling (contain redraw): < 3 s
Test 2: human Rhodopsin Model (HIN Format) Total Molecules: 3 Total Atoms: 5,401 Total Proteins: 3 Total Residues in Proteins: 340
Protein Superposition Merge: < 8 s Superposition of the 1HZX (Test 1 System; contain redraw): < 20 s
Ramachandran Plot Generate Plot: < 1 s
Side Chain Rotamer Modeling Auto Rotamer Search (Single-Point Calculations; Faster Method; Force Field: Amber94; Torsion Angles: gamma = 60º, delta = 60º, epsilon = 60º, zeta = 60º; Redraw Display: OFF; Others: Default): 6 + 1 Rotamers (CYS, SER, THR, VAL): < 16 s 36 + 1 Rotamers (ASP, PHE, HIS, ILE, LEU, ASN, TRP, TYR): < 1 m 19 s 216 + 1 Rotamers (GLU, MET, GLN): < 7 m 35 s 1,296 + 1 Rotamers (LYS, ARG): < 45 m 16 s
Test 3: human Retinol Binding Protein 1BRP (HIN Format) Total Molecules: 2 Total Atoms: 2,825 Total Proteins: 1 Total Residues in Proteins: 175
Interface Selection Selection of Contact Residues (Selection Target: Residues; Distance between Heavy Atoms: 4 Å ; Select Reference: OFF; Redraw Mode): < 1 s
Restraints Preview Restraints (Main Chain; 701 Restraints; Redraw Mode): < 5 s Restraints (Main Chain; 701 Restraints): < 5 s
Used System CPU: Intel Pentium4 3.20EGHz (FSB 800 MHz; L2 1MB) Memory: PC3200 (Dual Channel) CL3 4GB Chip Set: Intel I875P SCSI: Ultra320 HDD: Ultra320 36GB OS: Microsoft Windows XP Professional SP2 HyperChem: version 6.0.3
2005/06/06
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