Mon Oct 10 13:58:51 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+sph.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 = amb.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 13:58:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4389 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: 0.5069275 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): -2.837000 67.39000 ymin,ymax (A): -12.53300 39.02300 zmin,zma (A): -24.66200 44.90200 x,y,z range (A): 70.22700 51.55600 69.56400 scale (grids/A): 0.5069275 object centre (A): 32.27650 13.24500 10.12000 number of atom coordinates read : 4389 total number of charged atoms : 4235 net assigned charge : -2.499952 assigned positive charge : 660.1968 centred at (gu) : 87.97534 89.98692 91.80077 assigned negative charge : -662.6995 centred at (gu) : 88.05513 90.10998 91.87893 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7037 nv = 96 ne = 84 npr = 92148 no. pairs analyzed = 92148 no. exposed pairs = 5026 no. arc points = 33601 no. surface atoms = 1718 nbur = 2671 mkacc time = 0.1600000 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= 261 mr = 3958 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.3100000 number of dielectric boundary points 3326 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3408 ## 516 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 9576 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.8451676E-11 -3.1053179E-10 midg,1,midg; midg,igrid,midg 2.1703883E-10 -2.8362052E-10 1,midg,midg; igrid,midg,midg 2.2804784E-10 -1.1365647E-10 gauss-seidel spectral radius is 0.9800621 estimated iterations to convergence 59 setup time was (sec) 0.5000000 now iterating at: 13:58:51 rms-change max change #iterations 6.1208673E-02 10.51958 at 10iterations 3.7189254E-03 0.6024323 at 20iterations 4.5216380E-04 6.0825348E-02 at 30iterations 1.1732938E-04 1.5566826E-02 at 40iterations 3.4661389E-05 5.0826073E-03 at 50iterations finished qdiffx linear iterations at : 13:58:54 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 3.4661389E-05 5.0826073E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 13:58:55 3.504u 0.167s 0:04.22 86.7% 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 13:58:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4389 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: 1.520783 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): -2.837000 67.39000 ymin,ymax (A): -12.53300 39.02300 zmin,zma (A): -24.66200 44.90200 x,y,z range (A): 70.22700 51.55600 69.56400 scale (grids/A): 1.520783 object centre (A): 32.27650 13.24500 10.12000 number of atom coordinates read : 4389 total number of charged atoms : 4235 net assigned charge : -2.499952 assigned positive charge : 660.1968 centred at (gu) : 83.92517 89.95961 95.40123 assigned negative charge : -662.6995 centred at (gu) : 84.16493 90.32951 95.63637 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 80756 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33601 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23962 mr = 58081 m= 2161 mr = 16866 m= 46 mr = 1095 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1365 time to turn everything in is 0.4000000 number of dielectric boundary points 30883 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 465 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 31842 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) : 0.5069275 object centre at (A) : 32.27650 13.24500 10.12000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.8114422E-03 -1.4250968E-02 midg,1,midg; midg,igrid,midg 3.6785239E-03 -9.7114341E-03 1,midg,midg; igrid,midg,midg 1.5979987E-02 -6.7028548E-03 gauss-seidel spectral radius is 0.9980199 estimated iterations to convergence 179 setup time was (sec) 0.6100000 now iterating at: 13:58:56 rms-change max change #iterations 3.519171 179.6421 at 10iterations 1.411484 51.59441 at 20iterations 0.5685349 18.39412 at 30iterations 0.2284923 8.814424 at 40iterations 9.2071027E-02 3.117594 at 50iterations 3.6977828E-02 1.187843 at 60iterations 1.4926769E-02 0.4871998 at 70iterations 6.0611246E-03 0.2209282 at 80iterations 2.5014505E-03 8.2909107E-02 at 90iterations 1.0586836E-03 3.7463665E-02 at 100iterations 4.7963337E-04 1.6654968E-02 at 110iterations 2.3796057E-04 8.4152222E-03 at 120iterations finished qdiffx linear iterations at : 13:59:03 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 2.3796057E-04 8.4152222E-03 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 13:59:03 7.686u 0.175s 0:08.50 92.3% 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 13:59:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4389 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: 2.281174 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): -2.837000 67.39000 ymin,ymax (A): -12.53300 39.02300 zmin,zma (A): -24.66200 44.90200 x,y,z range (A): 70.22700 51.55600 69.56400 scale (grids/A): 2.281174 object centre (A): 32.27650 13.24500 10.12000 number of atom coordinates read : 4389 total number of charged atoms : 4235 net assigned charge : -2.499952 assigned positive charge : 660.1968 centred at (gu) : 80.88743 89.93926 98.10149 assigned negative charge : -662.6995 centred at (gu) : 81.24727 90.49424 98.45443 start vw surface at 0.1200000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 188680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33601 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 86332 mr = 142177 m= 22074 mr = 69679 m= 3255 mr = 16685 m= 124 mr = 2191 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 4391 time to turn everything in is 0.9400000 number of dielectric boundary points 69720 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 33784 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) : 1.520783 object centre at (A) : 32.27650 13.24500 10.12000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2432046 -0.3113650 midg,1,midg; midg,igrid,midg 3.9277367E-02 -0.1584470 1,midg,midg; igrid,midg,midg 0.3315147 -0.3042912 gauss-seidel spectral radius is 0.9991115 estimated iterations to convergence 265 setup time was (sec) 1.170000 now iterating at: 13:59:05 rms-change max change #iterations 9.480476 412.5862 at 10iterations 5.293505 126.1433 at 20iterations 2.936900 64.72459 at 30iterations 1.624668 34.57402 at 40iterations 0.8934242 18.74898 at 50iterations 0.4915433 9.237644 at 60iterations 0.2696266 5.128838 at 70iterations 0.1474065 2.802841 at 80iterations 8.0719188E-02 1.594632 at 90iterations 4.4212293E-02 0.8949209 at 100iterations 2.4150955E-02 0.4469070 at 110iterations 1.3241257E-02 0.2759800 at 120iterations 7.2634085E-03 0.1441650 at 130iterations 3.9973925E-03 7.4205399E-02 at 140iterations 2.2313576E-03 4.2168140E-02 at 150iterations 1.2618165E-03 2.4936676E-02 at 160iterations 7.3569972E-04 1.4343262E-02 at 170iterations 4.4388368E-04 8.1748962E-03 at 180iterations finished qdiffx linear iterations at : 13:59:16 total time elapsed so far: 12.70000 # loops : 180 mean,max change (kT/e) : 4.4388368E-04 8.1748962E-03 energy calculations done at 12.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.84000 DelPhi exited at 13:59:17 12.843u 0.242s 0:13.42 97.4% 0+0k 0+0io 0pf+0w