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   Last Modified

   10 April 2017

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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.

Output log file from the Side Chain Rotamer Modeling program

Number of Rotamers Methods Small Size (Glucagon, 1BH0) Middle Size (PPARg, 3PRG) Large Size (COX, 6COX-A)
29 Residues, 470 Atoms 267 Residues, 4361 Atoms 557 Residues, 9057 Atoms (HEM x 1, MAG x 4, S58 x 1)
6 + 1(Original) Single Point Faster 00m 01s (Ser2) 00m 04s (Val201) 00m 10s (Ser38)
Conventional 00m 01s (Ser2) 00m 17s (Val201) 01m 04s (Ser38)
6 + 1(Original) Geometry Optimization 00m 08s (Ser2) 00m 24s (Val201) 02m 33s (Ser38)
36 + 1(Original) Single Point Faster 00m 07s (His1) 00m 25s (His202) 00m 55s (Asn34)
Conventional 00m 07s (His1) 01m 30s (His202) 05m 37s (Asn34)
36 + 1(Original) Geometry Optimization 01m 12s (His1) 08m 00s (His202) 38m 14s (Asn34)
216 + 1(Original) Single Point Faster 00m 40s (Gln3) 02m 26s (Glu207) 05m 25s (Gln42)
Conventional 00m 44s (Gln3) 08m 49s (Glu207) 32m 58s (Gln42)
216 + 1(Original) Geometry Optimization 05m 54s (Gln3) 41m 27s (Glu207) 04h 20m 05s (Gln42)
1296 + 1(Original) Single Point Faster 04m 03s (Lys12) 14m 52s (Arg212) 32m 49s (Lys56)
Conventional 04m 23s (Lys12) 52m 41s (Arg212) 03h 16m 43s (Lys56)
1296 + 1(Original) Geometry Optimization - (Lys12) - (Arg212) - (Lys56)

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 7.51

 

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 = 60, delta =  60, epsilon = 60, zeta = 60; 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 ; 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 6.03

 

 

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