Wed Dec 21 14:21:37 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 14:21:38 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1913 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 14 has a net charge of 0.0730 !!! WARNING: ARG 41 has a net charge of -0.0090 !!! WARNING: LYS 70 has a net charge of 0.0730 !!! WARNING: LYS 106 has a net charge of 0.1210 !!! WARNING: GLN 117 has a net charge of 0.0170 !!! WARNING: LYS 154 has a net charge of 0.0730 !!! WARNING: LYS 169 has a net charge of 0.1210 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6432844 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): -4.688000 35.27500 ymin,ymax (A): -3.644000 47.27800 zmin,zma (A): -24.28500 31.05600 x,y,z range (A): 39.96300 50.92200 55.34100 scale (grids/A): 0.6432844 object centre (A): 15.29350 21.81700 3.385500 number of atom coordinates read : 1913 total number of charged atoms : 1781 net assigned charge : -2.510995 assigned positive charge : 279.0171 centred at (gu) : 90.40396 92.91096 90.10606 assigned negative charge : -281.5283 centred at (gu) : 90.52708 93.09268 90.11436 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5520 nv = 96 ne = 84 npr = 39612 no. pairs analyzed = 39612 no. exposed pairs = 2406 no. arc points = 16695 no. surface atoms = 818 nbur = 1095 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 292 mr = 3127 m= 0 mr = 54 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.1700000 number of dielectric boundary points 2631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1643 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 6352 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5440978E-09 -4.2075858E-09 midg,1,midg; midg,igrid,midg 6.8859904E-09 -3.8436294E-08 1,midg,midg; igrid,midg,midg 7.0877539E-09 -1.6107501E-08 gauss-seidel spectral radius is 0.9874195 estimated iterations to convergence 73 setup time was (sec) 0.5600000 now iterating at: 14:21:39 rms-change max change #iterations 0.1238984 18.58392 at 10iterations 1.2464020E-02 2.242783 at 20iterations 1.2408352E-03 0.2208343 at 30iterations 1.2425227E-04 2.0548314E-02 at 40iterations 1.2499723E-05 2.0675659E-03 at 50iterations finished qdiffx linear iterations at : 14:21:43 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 1.2499723E-05 2.0675659E-03 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 14:21:58 4.030u 0.419s 0:20.57 21.5% 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 Wed Dec 21 2011 at 14:22:00 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1913 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 14 has a net charge of 0.0730 !!! WARNING: ARG 41 has a net charge of -0.0090 !!! WARNING: LYS 70 has a net charge of 0.0730 !!! WARNING: LYS 106 has a net charge of 0.1210 !!! WARNING: GLN 117 has a net charge of 0.0170 !!! WARNING: LYS 154 has a net charge of 0.0730 !!! WARNING: LYS 169 has a net charge of 0.1210 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.929853 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): -4.688000 35.27500 ymin,ymax (A): -3.644000 47.27800 zmin,zma (A): -24.28500 31.05600 x,y,z range (A): 39.96300 50.92200 55.34100 scale (grids/A): 1.929853 object centre (A): 15.29350 21.81700 3.385500 number of atom coordinates read : 1913 total number of charged atoms : 1781 net assigned charge : -2.510995 assigned positive charge : 279.0171 centred at (gu) : 91.21203 98.73264 90.31841 assigned negative charge : -281.5283 centred at (gu) : 91.58136 99.27804 90.34306 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 58965 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16695 grid for indexing accessible points = 1.400000 m= 22920 mr = 41036 m= 3797 mr = 17842 m= 246 mr = 2526 m= 2 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1496 time to turn everything in is 0.3700000 number of dielectric boundary points 24401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 14046 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) : 0.6432844 object centre at (A) : 15.29350 21.81700 3.385500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5734248E-02 1.0384517E-03 midg,1,midg; midg,igrid,midg 1.8640082E-02 -3.1118620E-02 1,midg,midg; igrid,midg,midg 3.7268416E-03 -8.5948501E-03 gauss-seidel spectral radius is 0.9985865 estimated iterations to convergence 211 setup time was (sec) 0.7300000 now iterating at: 14:22:01 rms-change max change #iterations 3.634821 163.1483 at 10iterations 1.678357 60.43589 at 20iterations 0.7778491 30.59930 at 30iterations 0.3597872 13.06834 at 40iterations 0.1664059 6.402452 at 50iterations 7.6555744E-02 3.451772 at 60iterations 3.5349399E-02 1.377537 at 70iterations 1.6329153E-02 0.5755043 at 80iterations 7.5627971E-03 0.2554674 at 90iterations 3.4938352E-03 0.1214533 at 100iterations 1.6121587E-03 5.7865143E-02 at 110iterations 7.4811379E-04 2.7954102E-02 at 120iterations finished qdiffx linear iterations at : 14:22:11 total time elapsed so far: 10.43000 # loops : 120 mean,max change (kT/e) : 7.4811379E-04 2.7954102E-02 energy calculations done at 10.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.57000 DelPhi exited at 14:22:22 10.569u 0.427s 0:22.81 48.1% 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 14:22:24 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1913 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 14 has a net charge of 0.0730 !!! WARNING: ARG 41 has a net charge of -0.0090 !!! WARNING: LYS 70 has a net charge of 0.0730 !!! WARNING: LYS 106 has a net charge of 0.1210 !!! WARNING: GLN 117 has a net charge of 0.0170 !!! WARNING: LYS 154 has a net charge of 0.0730 !!! WARNING: LYS 169 has a net charge of 0.1210 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.894780 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): -4.688000 35.27500 ymin,ymax (A): -3.644000 47.27800 zmin,zma (A): -24.28500 31.05600 x,y,z range (A): 39.96300 50.92200 55.34100 scale (grids/A): 2.894780 object centre (A): 15.29350 21.81700 3.385500 number of atom coordinates read : 1913 total number of charged atoms : 1781 net assigned charge : -2.510995 assigned positive charge : 279.0171 centred at (gu) : 91.81801 103.0990 90.47774 assigned negative charge : -281.5283 centred at (gu) : 92.37215 103.9172 90.51469 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 136095 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16695 grid for indexing accessible points = 1.400000 m= 72212 mr = 98852 m= 28440 mr = 60714 m= 6885 mr = 23928 m= 1001 mr = 5394 m= 87 mr = 763 m= 2 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 5259 time to turn everything in is 0.9100000 number of dielectric boundary points 55015 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 14248 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) : 1.929853 object centre at (A) : 15.29350 21.81700 3.385500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6748771 -4.5345351E-02 midg,1,midg; midg,igrid,midg 0.1516761 -0.2672419 1,midg,midg; igrid,midg,midg 2.1264851E-02 -5.5133935E-02 gauss-seidel spectral radius is 0.9992310 estimated iterations to convergence 285 setup time was (sec) 1.320000 now iterating at: 14:22:27 rms-change max change #iterations 8.579824 535.7648 at 10iterations 4.921698 140.7380 at 20iterations 2.806615 64.32140 at 30iterations 1.590261 35.43933 at 40iterations 0.9062278 23.05540 at 50iterations 0.5143794 10.47149 at 60iterations 0.2925177 6.081629 at 70iterations 0.1661582 3.469215 at 80iterations 9.3956508E-02 1.900032 at 90iterations 5.3461745E-02 1.102230 at 100iterations 3.0333249E-02 0.6026344 at 110iterations 1.7208725E-02 0.3690672 at 120iterations 9.7730244E-03 0.1916660 at 130iterations 5.5267904E-03 0.1119986 at 140iterations 3.1413701E-03 6.6333771E-02 at 150iterations 1.7824540E-03 3.7132502E-02 at 160iterations 1.0128783E-03 2.0881653E-02 at 170iterations 5.7508500E-04 1.2825012E-02 at 180iterations finished qdiffx linear iterations at : 14:22:41 total time elapsed so far: 15.66000 # loops : 180 mean,max change (kT/e) : 5.7508500E-04 1.2825012E-02 energy calculations done at 15.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.79000 DelPhi exited at 14:22:48 15.792u 0.401s 0:23.59 68.6% 0+0k 0+0io 0pf+0w