Sat Oct 15 12:44:28 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 Sat Oct 15 2011 at 12:44:28 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5661 !!! WARNING: HIR 697 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5104528 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): 8.287999 77.77900 ymin,ymax (A): -30.69000 33.08800 zmin,zma (A): -19.33300 50.40900 x,y,z range (A): 69.49100 63.77800 69.74200 scale (grids/A): 0.5104528 object centre (A): 43.03350 1.199000 15.53800 number of atom coordinates read : 5661 total number of charged atoms : 5493 net assigned charge : -3.485984 assigned positive charge : 853.1807 centred at (gu) : 89.81239 89.50645 89.24798 assigned negative charge : -856.6737 centred at (gu) : 89.75012 89.57706 89.29025 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 9382 nv = 96 ne = 84 npr = 113625 no. pairs analyzed = 113625 no. exposed pairs = 7185 no. arc points = 49491 no. surface atoms = 2406 nbur = 3255 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 331 mr = 4852 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 4859 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4824 ## 685 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 12547 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.7285000E-11 -1.4964260E-10 midg,1,midg; midg,igrid,midg 1.8906521E-10 -2.3810759E-10 1,midg,midg; igrid,midg,midg -2.5765584E-10 1.3303676E-10 gauss-seidel spectral radius is 0.9804381 estimated iterations to convergence 59 setup time was (sec) 0.5800000 now iterating at: 12:44:29 rms-change max change #iterations 7.4469835E-02 11.28848 at 10iterations 4.4353749E-03 0.5898514 at 20iterations 5.6913559E-04 0.1258812 at 30iterations 1.7742872E-04 4.0594101E-02 at 40iterations 6.1068604E-05 1.3490677E-02 at 50iterations finished qdiffx linear iterations at : 12:44:33 total time elapsed so far: 3.760000 # loops : 50 mean,max change (kT/e) : 6.1068604E-05 1.3490677E-02 energy calculations done at 3.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.890000 DelPhi exited at 12:44:34 3.896u 0.246s 0:06.02 68.6% 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 Sat Oct 15 2011 at 12:44:34 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5661 !!! WARNING: HIR 697 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.531358 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): 8.287999 77.77900 ymin,ymax (A): -30.69000 33.08800 zmin,zma (A): -19.33300 50.40900 x,y,z range (A): 69.49100 63.77800 69.74200 scale (grids/A): 1.531358 object centre (A): 43.03350 1.199000 15.53800 number of atom coordinates read : 5661 total number of charged atoms : 5493 net assigned charge : -3.485984 assigned positive charge : 853.1807 centred at (gu) : 89.43536 88.51752 87.74226 assigned negative charge : -856.6737 centred at (gu) : 89.24997 88.73070 87.87045 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 106621 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49491 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 30436 mr = 73285 m= 2525 mr = 19875 m= 38 mr = 943 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 980 time to turn everything in is 0.5300000 number of dielectric boundary points 45517 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 684 ## 13 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 41310 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) : 0.5104528 object centre at (A) : 43.03350 1.199000 15.53800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3672961E-02 -1.8875845E-02 midg,1,midg; midg,igrid,midg 3.4773643E-03 -3.1614113E-03 1,midg,midg; igrid,midg,midg -1.8162332E-02 1.9545669E-03 gauss-seidel spectral radius is 0.9981962 estimated iterations to convergence 187 setup time was (sec) 0.7900000 now iterating at: 12:44:35 rms-change max change #iterations 4.207376 152.1889 at 10iterations 1.753778 56.75326 at 20iterations 0.7330627 20.75598 at 30iterations 0.3075811 8.563301 at 40iterations 0.1284317 3.894653 at 50iterations 5.3956114E-02 1.823944 at 60iterations 2.2584273E-02 0.6516285 at 70iterations 9.5108841E-03 0.2866554 at 80iterations 4.0229354E-03 0.1277142 at 90iterations 1.7362520E-03 5.6514740E-02 at 100iterations 7.6618436E-04 2.6800156E-02 at 110iterations 3.6312488E-04 1.5254974E-02 at 120iterations finished qdiffx linear iterations at : 12:44:47 total time elapsed so far: 8.850000 # loops : 120 mean,max change (kT/e) : 3.6312488E-04 1.5254974E-02 energy calculations done at 8.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.990000 DelPhi exited at 12:44:48 8.990u 0.285s 0:13.84 66.9% 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 Sat Oct 15 2011 at 12:44:48 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5661 !!! WARNING: HIR 697 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.297038 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): 8.287999 77.77900 ymin,ymax (A): -30.69000 33.08800 zmin,zma (A): -19.33300 50.40900 x,y,z range (A): 69.49100 63.77800 69.74200 scale (grids/A): 2.297038 object centre (A): 43.03350 1.199000 15.53800 number of atom coordinates read : 5661 total number of charged atoms : 5493 net assigned charge : -3.485984 assigned positive charge : 853.1807 centred at (gu) : 89.15237 87.77605 86.61320 assigned negative charge : -856.6737 centred at (gu) : 88.87479 88.09593 86.80576 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 248593 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49491 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 110227 mr = 180251 m= 26860 mr = 85291 m= 3438 mr = 18818 m= 164 mr = 1997 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 3084 time to turn everything in is 1.290000 number of dielectric boundary points 102892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 68 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 43803 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) : 1.531358 object centre at (A) : 43.03350 1.199000 15.53800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5098557 -0.5392994 midg,1,midg; midg,igrid,midg 4.8372421E-02 -4.8411157E-02 1,midg,midg; igrid,midg,midg -0.6704057 1.9363714E-02 gauss-seidel spectral radius is 0.9992124 estimated iterations to convergence 281 setup time was (sec) 1.600000 now iterating at: 12:44:51 rms-change max change #iterations 11.37904 362.3734 at 10iterations 6.661097 174.2386 at 20iterations 3.889603 93.11341 at 30iterations 2.247560 49.36915 at 40iterations 1.294688 26.52926 at 50iterations 0.7440351 14.75762 at 60iterations 0.4263331 8.377011 at 70iterations 0.2436340 4.399323 at 80iterations 0.1390683 2.421524 at 90iterations 7.9239190E-02 1.352579 at 100iterations 4.5089412E-02 0.8422852 at 110iterations 2.5680359E-02 0.4616823 at 120iterations 1.4614497E-02 0.2454262 at 130iterations 8.2866028E-03 0.1475601 at 140iterations 4.7155959E-03 7.9473495E-02 at 150iterations 2.6799715E-03 4.7603607E-02 at 160iterations 1.5277725E-03 2.4719238E-02 at 170iterations 8.7624270E-04 1.5228271E-02 at 180iterations finished qdiffx linear iterations at : 12:45:11 total time elapsed so far: 15.22000 # loops : 180 mean,max change (kT/e) : 8.7624270E-04 1.5228271E-02 energy calculations done at 15.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.35000 DelPhi exited at 12:45:11 15.347u 0.305s 0:23.36 66.9% 0+0k 0+0io 0pf+0w