log started: Mon Apr  3 15:00:05 2006

Log file: ./LEaP-Tutorial-2.log
> 
> verbosity 2
Verbosity level: 2
> 
> AIB = loadmol2 5-Charges-2conf-RBRA-4-INTRA-MCC/Mol_m1-o1-sm.mol2
Loading Mol2 file: ./5-Charges-2conf-RBRA-4-INTRA-MCC/Mol_m1-o1-sm.mol2
> NAIB = loadmol2 6-Charges-2conf-RBRA-4-INTER-MCC1/Mol_MM1/Mol_m2-o1-mm1.mol2
Loading Mol2 file: ./6-Charges-2conf-RBRA-4-INTER-MCC1/Mol_MM1/Mol_m2-o1-mm1.mol2
> CAIB = loadmol2 6-Charges-2conf-RBRA-4-INTER-MCC2/Mol_MM1/Mol_m2-o1-mm1.mol2
Loading Mol2 file: ./6-Charges-2conf-RBRA-4-INTER-MCC2/Mol_MM1/Mol_m2-o1-mm1.mol2
> 
> charge AIB
Total unperturbed charge: 0.000200
Total perturbed charge:   0.000200
> charge NAIB
Total unperturbed charge: 1.000200
Total perturbed charge:   1.000200
> charge CAIB
Total unperturbed charge: -0.999800
Total perturbed charge:   -0.999800
> 
> # set general information for AIB
> set AIB name "AIB"
> set AIB.1 restype protein
> set AIB.1 name "AIB"
> set AIB head AIB.1.N
> set AIB tail AIB.1.C
> set AIB.1 connect0 AIB.1.N
> set AIB.1 connect1 AIB.1.C
> # set FF atom types for AIB
> set AIB.1.N type N
> set AIB.1.H type H
> set AIB.1.CA type CT
> set AIB.1.CB1 type CT
> set AIB.1.HB11 type HC
> set AIB.1.HB12 type HC
> set AIB.1.HB13 type HC
> set AIB.1.CB2 type CT
> set AIB.1.HB21 type HC
> set AIB.1.HB22 type HC
> set AIB.1.HB23 type HC
> set AIB.1.C type C
> set AIB.1.O type O
> # save the OFF library for AIB
> saveoff AIB AIB.off
 Creating AIB.off
Saving AIB.
Building topology.
Building atom parameters.
> 
> # set general information for NAIB
> set NAIB name "NAIB"
> set NAIB.1 restype protein
> set NAIB.1 name "NAIB"
> # head = null
> set NAIB tail NAIB.1.C
> set NAIB.1 connect0 NAIB.1.N
> set NAIB.1 connect1 NAIB.1.C
> # set FF atom types for NAIB
> set NAIB.1.N type N3
> set NAIB.1.H1 type H
> set NAIB.1.H2 type H
> set NAIB.1.H3 type H
> set NAIB.1.CA type CT
> set NAIB.1.CB1 type CT
> set NAIB.1.HB11 type HC
> set NAIB.1.HB12 type HC
> set NAIB.1.HB13 type HC
> set NAIB.1.CB2 type CT
> set NAIB.1.HB21 type HC
> set NAIB.1.HB22 type HC
> set NAIB.1.HB23 type HC
> set NAIB.1.C type C
> set NAIB.1.O type O
> # save the OFF library for NAIB
> saveoff NAIB NAIB.off
 Creating NAIB.off
Saving NAIB.
Building topology.
Building atom parameters.
> 
> # set general information for CAIB
> set CAIB name "CAIB"
> set CAIB.1 restype protein
> set CAIB.1 name "CAIB"
> set CAIB head CAIB.1.N
> # tail = null
> set CAIB.1 connect0 CAIB.1.N
> set CAIB.1 connect1 CAIB.1.C
> # set FF atom types for CAIB
> set CAIB.1.N type N
> set CAIB.1.H type H
> set CAIB.1.CA type CT
> set CAIB.1.CB1 type CT
> set CAIB.1.HB11 type HC
> set CAIB.1.HB12 type HC
> set CAIB.1.HB13 type HC
> set CAIB.1.CB2 type CT
> set CAIB.1.HB21 type HC
> set CAIB.1.HB22 type HC
> set CAIB.1.HB23 type HC
> set CAIB.1.C type C
> set CAIB.1.O type O2
> set CAIB.1.OXT type O2
> # save the OFF library for CAIB
> saveoff CAIB CAIB.off
 Creating CAIB.off
Saving CAIB.
Building topology.
Building atom parameters.
>  
> edit NAIB
Unit Editor: Gradient RMS=931.090457
Unit Editor: Gradient RMS=714.834159
Unit Editor: Gradient RMS=205.450968
Unit Editor: Gradient RMS=429.868915
Unit Editor: Gradient RMS=1322.534022
Unit Editor: Gradient RMS=2.914119
Unit Editor: Gradient RMS=1.652014
Unit Editor: Gradient RMS=0.399715
Unit Editor: Gradient RMS=0.609089
Unit Editor: Gradient RMS=0.158623
Unit Editor: Gradient RMS=6.281817
Unit Editor: Gradient RMS=16.776870
Unit Editor: Gradient RMS=22.056479
Unit Editor: Gradient RMS=45.150933
Unit Editor: Gradient RMS=0.187797
Unit Editor: Gradient RMS=0.354325
Unit Editor: Gradient RMS=0.075915
Unit Editor: Gradient RMS=0.028221
Unit Editor: Search terminated when RMS gradient became small enough!
Unit Editor: Number of conjugate gradient steps taken: 178
> edit CAIB
Unit Editor: Gradient RMS=2812.724180
Unit Editor: Gradient RMS=86.212603
Unit Editor: Gradient RMS=2.227216
Unit Editor: Gradient RMS=0.369334
Unit Editor: Gradient RMS=0.223533
Unit Editor: Search terminated when RMS gradient became small enough!
Unit Editor: Number of conjugate gradient steps taken: 42
>
> saveoff NAIB NAIB.off
Saving NAIB.
Building topology.
Building atom parameters.
> saveoff CAIB CAIB.off
Saving CAIB.
Building topology.
Building atom parameters.
>
> EXAMPLE = sequence { NAIB AIB CAIB }
Sequence: NAIB
Sequence: AIB
Joining NAIB - AIB
Sequence: CAIB
Joining AIB - CAIB
> impose EXAMPLE {1 2 3}{{N CA C N 180.0}{C N CA C 180.0}{CA C N CA 180.0}{CA C N CA 180.0}{N CA C OXT 180.0}{C CA N H1 180.0}}
> quit
	Quit