Mon Oct 10 22:36:07 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 22:36:07 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2673 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: ASP 298 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6054216 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): -19.93500 32.22600 ymin,ymax (A): 18.03600 76.83800 zmin,zma (A): 9.929000 52.54100 x,y,z range (A): 52.16100 58.80200 42.61200 scale (grids/A): 0.6054216 object centre (A): 6.145501 47.43700 31.23500 number of atom coordinates read : 2673 total number of charged atoms : 2526 net assigned charge : 2.406018 assigned positive charge : 402.6748 centred at (gu) : 91.05003 89.24271 89.82829 assigned negative charge : -400.2693 centred at (gu) : 91.02593 89.54942 90.02674 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6398 nv = 96 ne = 84 npr = 54591 no. pairs analyzed = 54591 no. exposed pairs = 3138 no. arc points = 21856 no. surface atoms = 1063 nbur = 1610 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 275 mr = 3580 m= 0 mr = 29 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3700000 number of dielectric boundary points 3064 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2148 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7976 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0119710E-08 -7.5973325E-09 midg,1,midg; midg,igrid,midg 1.6973132E-08 -1.0923157E-08 1,midg,midg; igrid,midg,midg 4.3567022E-11 2.7604521E-09 gauss-seidel spectral radius is 0.9858791 estimated iterations to convergence 69 setup time was (sec) 0.6500000 now iterating at: 22:36:08 rms-change max change #iterations 0.1183378 17.44036 at 10iterations 1.0854393E-02 1.597748 at 20iterations 1.3257617E-03 0.2733841 at 30iterations 3.1779526E-04 7.9006195E-02 at 40iterations 9.1257505E-05 2.3231506E-02 at 50iterations finished qdiffx linear iterations at : 22:36:11 total time elapsed so far: 4.080000 # loops : 50 mean,max change (kT/e) : 9.1257505E-05 2.3231506E-02 energy calculations done at 4.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 22:36:12 4.273u 0.231s 0:05.14 87.5% 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 22:36:12 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2673 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: ASP 298 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.816265 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): -19.93500 32.22600 ymin,ymax (A): 18.03600 76.83800 zmin,zma (A): 9.929000 52.54100 x,y,z range (A): 52.16100 58.80200 42.61200 scale (grids/A): 1.816265 object centre (A): 6.145501 47.43700 31.23500 number of atom coordinates read : 2673 total number of charged atoms : 2526 net assigned charge : 2.406018 assigned positive charge : 402.6748 centred at (gu) : 93.14950 87.72796 89.48463 assigned negative charge : -400.2693 centred at (gu) : 93.07761 88.64790 90.08003 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 70059 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21856 grid for indexing accessible points = 1.400000 m= 23511 mr = 49222 m= 3226 mr = 17404 m= 144 mr = 2031 m= 5 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 2173 time to turn everything in is 0.6200000 number of dielectric boundary points 28250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 19718 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) : 0.6054216 object centre at (A) : 6.145501 47.43700 31.23500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5607867E-02 5.1534903E-04 midg,1,midg; midg,igrid,midg -1.5204071E-02 -5.8196500E-02 1,midg,midg; igrid,midg,midg 1.6048652E-03 -1.7705621E-03 gauss-seidel spectral radius is 0.9985040 estimated iterations to convergence 205 setup time was (sec) 0.9700000 now iterating at: 22:36:13 rms-change max change #iterations 3.943821 184.7798 at 10iterations 1.776703 68.81746 at 20iterations 0.8035961 32.74869 at 30iterations 0.3646417 12.28596 at 40iterations 0.1640819 6.497231 at 50iterations 7.4427374E-02 2.350593 at 60iterations 3.3929296E-02 1.125526 at 70iterations 1.5415170E-02 0.4871788 at 80iterations 7.0486963E-03 0.2391357 at 90iterations 3.3173335E-03 0.1115475 at 100iterations 1.5921362E-03 5.9333801E-02 at 110iterations 8.0556015E-04 3.3618927E-02 at 120iterations finished qdiffx linear iterations at : 22:36:22 total time elapsed so far: 9.450000 # loops : 120 mean,max change (kT/e) : 8.0556015E-04 3.3618927E-02 energy calculations done at 9.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.630000 DelPhi exited at 22:36:22 9.635u 0.290s 0:10.22 97.0% 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 22:36:22 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2673 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: ASP 298 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.724397 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): -19.93500 32.22600 ymin,ymax (A): 18.03600 76.83800 zmin,zma (A): 9.929000 52.54100 x,y,z range (A): 52.16100 58.80200 42.61200 scale (grids/A): 2.724397 object centre (A): 6.145501 47.43700 31.23500 number of atom coordinates read : 2673 total number of charged atoms : 2526 net assigned charge : 2.406018 assigned positive charge : 402.6748 centred at (gu) : 94.72435 86.59166 89.22675 assigned negative charge : -400.2693 centred at (gu) : 94.61623 87.97173 90.11994 start vw surface at 0.1600000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 162540 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21856 grid for indexing accessible points = 1.400000 m= 78915 mr = 119333 m= 25839 mr = 64869 m= 5602 mr = 20831 m= 626 mr = 4280 m= 27 mr = 426 m= 0 mr = 1 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 7407 time to turn everything in is 1.400000 number of dielectric boundary points 63809 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 20203 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) : 1.816265 object centre at (A) : 6.145501 47.43700 31.23500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2770901 4.3671254E-02 midg,1,midg; midg,igrid,midg -0.6496699 -0.6839350 1,midg,midg; igrid,midg,midg -2.2281663E-02 -5.4948982E-02 gauss-seidel spectral radius is 0.9992176 estimated iterations to convergence 282 setup time was (sec) 1.760000 now iterating at: 22:36:24 rms-change max change #iterations 9.363546 302.5387 at 10iterations 5.361330 135.9314 at 20iterations 3.046366 63.32260 at 30iterations 1.728218 35.20940 at 40iterations 0.9804254 20.32450 at 50iterations 0.5558739 10.46619 at 60iterations 0.3142442 5.871893 at 70iterations 0.1780830 3.331951 at 80iterations 0.1009159 1.913658 at 90iterations 5.7032499E-02 1.120102 at 100iterations 3.2307986E-02 0.6356230 at 110iterations 1.8365366E-02 0.3604790 at 120iterations 1.0456484E-02 0.2130699 at 130iterations 5.9991851E-03 0.1209106 at 140iterations 3.4968604E-03 8.0653191E-02 at 150iterations 2.0820911E-03 4.6741486E-02 at 160iterations 1.2870659E-03 3.3740997E-02 at 170iterations 8.3612761E-04 2.1694183E-02 at 180iterations finished qdiffx linear iterations at : 22:36:38 total time elapsed so far: 15.19000 # loops : 180 mean,max change (kT/e) : 8.3612761E-04 2.1694183E-02 energy calculations done at 15.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.38000 DelPhi exited at 22:36:38 15.380u 0.257s 0:16.01 97.6% 0+0k 0+0io 0pf+0w