Mon Oct 10 17:11:41 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 17:11:41 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3009 !!! WARNING: HIR 613 has a net charge of 0.5140 !!! WARNING: HIZ 617 has a net charge of 0.2000 !!! WARNING: HIZ 653 has a net charge of 0.2000 !!! WARNING: MG8 861 has a net charge of 1.4000 !!! WARNING: ZN8 862 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.6265290 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 48.50700 101.5160 ymin,ymax (A): -7.218000 49.60300 zmin,zma (A): -5.360000 47.96100 x,y,z range (A): 53.00900 56.82100 53.32100 scale (grids/A): 0.6265290 object centre (A): 75.01150 21.19250 21.30050 number of atom coordinates read : 3009 total number of charged atoms : 2867 net assigned charge : 5.714033 assigned positive charge : 464.2392 centred at (gu) : 89.03139 89.34879 90.89887 assigned negative charge : -458.5262 centred at (gu) : 89.04746 89.40950 91.04088 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7691 nv = 96 ne = 84 npr = 61426 no. pairs analyzed = 61426 no. exposed pairs = 3792 no. arc points = 26627 no. surface atoms = 1275 nbur = 1734 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 429 mr = 4136 m= 0 mr = 32 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2646 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9555 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5538493E-08 -9.8053805E-09 midg,1,midg; midg,igrid,midg 1.3114108E-08 -4.5617572E-11 1,midg,midg; igrid,midg,midg 8.8614653E-09 3.4088439E-09 gauss-seidel spectral radius is 0.9868414 estimated iterations to convergence 71 setup time was (sec) 0.5600000 now iterating at: 17:11:42 rms-change max change #iterations 0.1490598 25.87179 at 10iterations 1.4190461E-02 2.269501 at 20iterations 1.4115131E-03 0.1773893 at 30iterations 1.8622249E-04 2.3452759E-02 at 40iterations 3.9943498E-05 5.7239532E-03 at 50iterations finished qdiffx linear iterations at : 17:11:44 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 3.9943498E-05 5.7239532E-03 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 17:11:45 3.315u 0.161s 0:03.80 91.3% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 17:11:45 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3009 !!! WARNING: HIR 613 has a net charge of 0.5140 !!! WARNING: HIZ 617 has a net charge of 0.2000 !!! WARNING: HIZ 653 has a net charge of 0.2000 !!! WARNING: MG8 861 has a net charge of 1.4000 !!! WARNING: ZN8 862 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.879587 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 48.50700 101.5160 ymin,ymax (A): -7.218000 49.60300 zmin,zma (A): -5.360000 47.96100 x,y,z range (A): 53.00900 56.82100 53.32100 scale (grids/A): 1.879587 object centre (A): 75.01150 21.19250 21.30050 number of atom coordinates read : 3009 total number of charged atoms : 2867 net assigned charge : 5.714033 assigned positive charge : 464.2392 centred at (gu) : 87.09325 88.04609 92.69571 assigned negative charge : -458.5262 centred at (gu) : 87.14211 88.22826 93.12199 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 83948 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26627 grid for indexing accessible points = 1.400000 m= 29592 mr = 57651 m= 4768 mr = 21269 m= 289 mr = 2897 m= 5 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 187 time to turn everything in is 0.6000000 number of dielectric boundary points 36685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 190 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 22509 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6265290 object centre at (A) : 75.01150 21.19250 21.30050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5816414E-02 -8.1703169E-03 midg,1,midg; midg,igrid,midg 1.5009046E-02 9.1204662E-03 1,midg,midg; igrid,midg,midg 1.1834330E-02 2.8429870E-03 gauss-seidel spectral radius is 0.9986418 estimated iterations to convergence 215 setup time was (sec) 0.9200000 now iterating at: 17:11:46 rms-change max change #iterations 4.672527 203.6941 at 10iterations 2.186157 77.82457 at 20iterations 1.028896 31.44424 at 30iterations 0.4823584 15.27081 at 40iterations 0.2254493 7.466812 at 50iterations 0.1061725 3.323845 at 60iterations 4.9984653E-02 1.497904 at 70iterations 2.3451122E-02 0.7714844 at 80iterations 1.1017852E-02 0.3340921 at 90iterations 5.1791607E-03 0.1654434 at 100iterations 2.4375215E-03 7.1119308E-02 at 110iterations 1.1510234E-03 3.3905029E-02 at 120iterations finished qdiffx linear iterations at : 17:11:53 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 1.1510234E-03 3.3905029E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 17:11:53 7.642u 0.267s 0:08.52 92.7% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 17:11:53 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3009 !!! WARNING: HIR 613 has a net charge of 0.5140 !!! WARNING: HIZ 617 has a net charge of 0.2000 !!! WARNING: HIZ 653 has a net charge of 0.2000 !!! WARNING: MG8 861 has a net charge of 1.4000 !!! WARNING: ZN8 862 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.819380 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 48.50700 101.5160 ymin,ymax (A): -7.218000 49.60300 zmin,zma (A): -5.360000 47.96100 x,y,z range (A): 53.00900 56.82100 53.32100 scale (grids/A): 2.819380 object centre (A): 75.01150 21.19250 21.30050 number of atom coordinates read : 3009 total number of charged atoms : 2867 net assigned charge : 5.714033 assigned positive charge : 464.2392 centred at (gu) : 85.63982 87.06891 94.04332 assigned negative charge : -458.5262 centred at (gu) : 85.71293 87.34221 94.68297 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 194853 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26627 grid for indexing accessible points = 1.400000 m= 95361 mr = 140846 m= 34858 mr = 76659 m= 8601 mr = 27436 m= 1271 mr = 6312 m= 65 mr = 848 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 594 time to turn everything in is 1.440000 number of dielectric boundary points 82892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 22936 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.879587 object centre at (A) : 75.01150 21.19250 21.30050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5455830 -1.3580113E-02 midg,1,midg; midg,igrid,midg 0.1476293 0.2277743 1,midg,midg; igrid,midg,midg 0.1232807 1.7956534E-02 gauss-seidel spectral radius is 0.9992726 estimated iterations to convergence 293 setup time was (sec) 1.730000 now iterating at: 17:11:55 rms-change max change #iterations 10.95502 374.2158 at 10iterations 6.493254 152.1199 at 20iterations 3.803940 78.98759 at 30iterations 2.224843 43.14375 at 40iterations 1.298773 28.00567 at 50iterations 0.7555677 14.00428 at 60iterations 0.4392647 8.511976 at 70iterations 0.2547960 4.566968 at 80iterations 0.1477589 2.593759 at 90iterations 8.5503414E-02 1.465170 at 100iterations 4.9520943E-02 0.8823881 at 110iterations 2.8685611E-02 0.5135193 at 120iterations 1.6572645E-02 0.2901721 at 130iterations 9.6017038E-03 0.1629920 at 140iterations 5.5647097E-03 8.9112282E-02 at 150iterations 3.2199125E-03 5.5620193E-02 at 160iterations 1.8648641E-03 3.4261227E-02 at 170iterations 1.0871617E-03 2.0847321E-02 at 180iterations finished qdiffx linear iterations at : 17:12:05 total time elapsed so far: 11.51000 # loops : 180 mean,max change (kT/e) : 1.0871617E-03 2.0847321E-02 energy calculations done at 11.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.68000 DelPhi exited at 17:12:06 11.687u 0.158s 0:12.17 97.2% 0+0k 0+0io 0pf+0w