Wed Dec 21 14:23:00 PST 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 Wed Dec 21 2011 at 14:23:01 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1954 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ARG 41 has a net charge of 0.0400 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: 0.6491256 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): -5.095000 34.47700 ymin,ymax (A): -3.459000 48.19700 zmin,zma (A): -24.11900 30.72400 x,y,z range (A): 39.57200 51.65600 54.84300 scale (grids/A): 0.6491256 object centre (A): 14.69100 22.36900 3.302501 number of atom coordinates read : 1954 total number of charged atoms : 1821 net assigned charge : 1.721005 assigned positive charge : 288.6921 centred at (gu) : 90.74706 92.55208 90.06078 assigned negative charge : -286.9712 centred at (gu) : 90.83719 92.72621 90.03359 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5609 nv = 96 ne = 84 npr = 40713 no. pairs analyzed = 40713 no. exposed pairs = 2447 no. arc points = 17252 no. surface atoms = 833 nbur = 1121 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 289 mr = 3112 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 2754 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1804 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 6627 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.8327368E-10 6.9177863E-09 midg,1,midg; midg,igrid,midg 1.3175095E-08 -2.7316771E-08 1,midg,midg; igrid,midg,midg 1.1627425E-08 -7.1699922E-09 gauss-seidel spectral radius is 0.9876435 estimated iterations to convergence 74 setup time was (sec) 0.8200000 now iterating at: 14:23:03 rms-change max change #iterations 0.1318745 22.88206 at 10iterations 1.3593167E-02 2.345978 at 20iterations 1.3719192E-03 0.2469279 at 30iterations 1.3867424E-04 2.1230698E-02 at 40iterations 1.4084625E-05 2.4223328E-03 at 50iterations finished qdiffx linear iterations at : 14:23:10 total time elapsed so far: 7.270000 # loops : 50 mean,max change (kT/e) : 1.4084625E-05 2.4223328E-03 energy calculations done at 7.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.490000 DelPhi exited at 14:23:12 7.490u 0.663s 0:10.40 78.3% 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 Wed Dec 21 2011 at 14:23:12 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1954 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ARG 41 has a net charge of 0.0400 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: 1.947377 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): -5.095000 34.47700 ymin,ymax (A): -3.459000 48.19700 zmin,zma (A): -24.11900 30.72400 x,y,z range (A): 39.57200 51.65600 54.84300 scale (grids/A): 1.947377 object centre (A): 14.69100 22.36900 3.302501 number of atom coordinates read : 1954 total number of charged atoms : 1821 net assigned charge : 1.721005 assigned positive charge : 288.6921 centred at (gu) : 92.24126 97.65611 90.18240 assigned negative charge : -286.9712 centred at (gu) : 92.51182 98.17870 90.10081 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 59923 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17252 grid for indexing accessible points = 1.400000 m= 21730 mr = 41224 m= 3309 mr = 16493 m= 139 mr = 2105 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1043 time to turn everything in is 0.6300000 number of dielectric boundary points 25237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 14393 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) : 0.6491256 object centre at (A) : 14.69100 22.36900 3.302501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3272443E-02 8.5763605E-03 midg,1,midg; midg,igrid,midg 3.2772053E-02 -1.5923630E-02 1,midg,midg; igrid,midg,midg 7.3503419E-03 -6.2311525E-03 gauss-seidel spectral radius is 0.9986130 estimated iterations to convergence 213 setup time was (sec) 1.060000 now iterating at: 14:23:14 rms-change max change #iterations 3.766582 176.6775 at 10iterations 1.751205 69.15719 at 20iterations 0.8171036 27.23543 at 30iterations 0.3810416 13.55807 at 40iterations 0.1763568 6.095412 at 50iterations 8.2019463E-02 2.879620 at 60iterations 3.8205124E-02 1.402304 at 70iterations 1.7831702E-02 0.5922518 at 80iterations 8.2882820E-03 0.2911224 at 90iterations 3.8307020E-03 0.1218567 at 100iterations 1.7833741E-03 6.0493231E-02 at 110iterations 8.3195738E-04 2.8844833E-02 at 120iterations finished qdiffx linear iterations at : 14:23:27 total time elapsed so far: 13.88000 # loops : 120 mean,max change (kT/e) : 8.3195738E-04 2.8844833E-02 energy calculations done at 13.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.10000 DelPhi exited at 14:23:27 14.107u 0.684s 0:15.23 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 Wed Dec 21 2011 at 14:23:27 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1954 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ARG 41 has a net charge of 0.0400 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: 2.921066 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): -5.095000 34.47700 ymin,ymax (A): -3.459000 48.19700 zmin,zma (A): -24.11900 30.72400 x,y,z range (A): 39.57200 51.65600 54.84300 scale (grids/A): 2.921066 object centre (A): 14.69100 22.36900 3.302501 number of atom coordinates read : 1954 total number of charged atoms : 1821 net assigned charge : 1.721005 assigned positive charge : 288.6921 centred at (gu) : 93.36185 101.4842 90.27366 assigned negative charge : -286.9712 centred at (gu) : 93.76773 102.2681 90.15126 start vw surface at 0.1400000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 138366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17252 grid for indexing accessible points = 1.400000 m= 70411 mr = 99893 m= 26108 mr = 58204 m= 5917 mr = 21567 m= 619 mr = 4485 m= 23 mr = 397 m= 0 mr = 7 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 3595 time to turn everything in is 1.800000 number of dielectric boundary points 56891 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 14568 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) : 1.947377 object centre at (A) : 14.69100 22.36900 3.302501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9858987 -2.4809331E-02 midg,1,midg; midg,igrid,midg 0.3343288 -0.1666689 1,midg,midg; igrid,midg,midg 5.0755974E-02 -4.3178458E-02 gauss-seidel spectral radius is 0.9992405 estimated iterations to convergence 286 setup time was (sec) 2.320000 now iterating at: 14:23:30 rms-change max change #iterations 8.801749 455.4793 at 10iterations 5.081784 141.6915 at 20iterations 2.909265 71.07903 at 30iterations 1.661967 39.45655 at 40iterations 0.9510812 19.32102 at 50iterations 0.5422906 10.88366 at 60iterations 0.3093434 6.306818 at 70iterations 0.1765497 3.363803 at 80iterations 0.1003794 2.077295 at 90iterations 5.7219882E-02 1.195308 at 100iterations 3.2623503E-02 0.7108397 at 110iterations 1.8551148E-02 0.3450898 at 120iterations 1.0554571E-02 0.2222672 at 130iterations 6.0209772E-03 0.1249094 at 140iterations 3.4258876E-03 6.2149048E-02 at 150iterations 1.9471307E-03 3.7506104E-02 at 160iterations 1.1095192E-03 2.0497203E-02 at 170iterations 6.3145801E-04 1.1896133E-02 at 180iterations finished qdiffx linear iterations at : 14:23:56 total time elapsed so far: 28.04000 # loops : 180 mean,max change (kT/e) : 6.3145801E-04 1.1896133E-02 energy calculations done at 28.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 28.26000 DelPhi exited at 14:23:57 28.260u 0.889s 0:29.50 98.7% 0+0k 0+0io 0pf+0w