Mon Oct 10 17:04:20 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 17:04:20 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3057 !!! WARNING: HIR 80 has a net charge of 0.5140 !!! WARNING: HIR 84 has a net charge of 0.5140 !!! WARNING: GLM 285 has a net charge of -0.0940 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: 0.5759120 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): 3.423000 65.23800 ymin,ymax (A): 13.08800 65.05500 zmin,zma (A): -25.82900 30.78700 x,y,z range (A): 61.81500 51.96700 56.61600 scale (grids/A): 0.5759120 object centre (A): 34.33050 39.07150 2.478999 number of atom coordinates read : 3057 total number of charged atoms : 2908 net assigned charge : -1.565983 assigned positive charge : 462.3409 centred at (gu) : 90.67404 91.43452 90.65898 assigned negative charge : -463.9082 centred at (gu) : 90.69005 91.53532 90.62852 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6735 nv = 96 ne = 84 npr = 61576 no. pairs analyzed = 61576 no. exposed pairs = 3929 no. arc points = 27883 no. surface atoms = 1316 nbur = 1741 mkacc time = 0.1300000 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 = 1.484000 m= 288 mr = 3492 m= 0 mr = 14 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3517 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2918 ## 366 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8591 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.4933321E-10 4.0350387E-10 midg,1,midg; midg,igrid,midg 1.2232342E-09 -3.2522094E-09 1,midg,midg; igrid,midg,midg 4.4781012E-11 -6.8493272E-10 gauss-seidel spectral radius is 0.9844530 estimated iterations to convergence 66 setup time was (sec) 0.5900000 now iterating at: 17:04:21 rms-change max change #iterations 9.7858019E-02 17.80819 at 10iterations 7.3575545E-03 1.204410 at 20iterations 5.7068031E-04 9.1308594E-02 at 30iterations 4.4635639E-05 6.5279007E-03 at 40iterations 4.1757203E-06 6.7138672E-04 at 50iterations finished qdiffx linear iterations at : 17:04:23 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 4.1757203E-06 6.7138672E-04 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 17:04:24 3.218u 0.146s 0:04.21 79.5% 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 17:04:24 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3057 !!! WARNING: HIR 80 has a net charge of 0.5140 !!! WARNING: HIR 84 has a net charge of 0.5140 !!! WARNING: GLM 285 has a net charge of -0.0940 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: 1.727736 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): 3.423000 65.23800 ymin,ymax (A): 13.08800 65.05500 zmin,zma (A): -25.82900 30.78700 x,y,z range (A): 61.81500 51.96700 56.61600 scale (grids/A): 1.727736 object centre (A): 34.33050 39.07150 2.478999 number of atom coordinates read : 3057 total number of charged atoms : 2908 net assigned charge : -1.565983 assigned positive charge : 462.3409 centred at (gu) : 92.02117 94.30279 91.97620 assigned negative charge : -463.9082 centred at (gu) : 92.06995 94.60558 91.88550 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73915 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27883 grid for indexing accessible points = 1.400000 m= 23597 mr = 49714 m= 2893 mr = 16478 m= 100 mr = 1625 m= 0 mr = 1 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 878 time to turn everything in is 0.5000000 number of dielectric boundary points 32687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 290 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 22523 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) : 0.5759120 object centre at (A) : 34.33050 39.07150 2.478999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7216038E-04 -1.4769082E-02 midg,1,midg; midg,igrid,midg 3.6677525E-03 -1.5888343E-02 1,midg,midg; igrid,midg,midg 2.5615873E-02 1.6613890E-03 gauss-seidel spectral radius is 0.9984059 estimated iterations to convergence 199 setup time was (sec) 0.7500000 now iterating at: 17:04:25 rms-change max change #iterations 3.848831 172.2455 at 10iterations 1.683405 66.37472 at 20iterations 0.7429270 29.16932 at 30iterations 0.3282537 11.07289 at 40iterations 0.1445273 4.517223 at 50iterations 6.3447088E-02 2.096238 at 60iterations 2.8044928E-02 0.9243784 at 70iterations 1.2336164E-02 0.3830290 at 80iterations 5.4565156E-03 0.1792928 at 90iterations 2.4005645E-03 8.2272500E-02 at 100iterations 1.0632735E-03 3.6357880E-02 at 110iterations 4.6815467E-04 1.6016006E-02 at 120iterations finished qdiffx linear iterations at : 17:04:31 total time elapsed so far: 6.860000 # loops : 120 mean,max change (kT/e) : 4.6815467E-04 1.6016006E-02 energy calculations done at 6.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.070000 DelPhi exited at 17:04:33 7.071u 0.182s 0:08.15 88.9% 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 Mon Oct 10 2011 at 17:04:33 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3057 !!! WARNING: HIR 80 has a net charge of 0.5140 !!! WARNING: HIR 84 has a net charge of 0.5140 !!! WARNING: GLM 285 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.591604 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): 3.423000 65.23800 ymin,ymax (A): 13.08800 65.05500 zmin,zma (A): -25.82900 30.78700 x,y,z range (A): 61.81500 51.96700 56.61600 scale (grids/A): 2.591604 object centre (A): 34.33050 39.07150 2.478999 number of atom coordinates read : 3057 total number of charged atoms : 2908 net assigned charge : -1.565983 assigned positive charge : 462.3409 centred at (gu) : 93.03148 96.45397 92.96396 assigned negative charge : -463.9082 centred at (gu) : 93.10485 96.90835 92.82825 start vw surface at 0.1700000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 171807 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27883 grid for indexing accessible points = 1.400000 m= 79515 mr = 121990 m= 24843 mr = 63009 m= 4840 mr = 18963 m= 394 mr = 3442 m= 11 mr = 195 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 3047 time to turn everything in is 1.270000 number of dielectric boundary points 73811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 23253 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) : 1.727736 object centre at (A) : 34.33050 39.07150 2.478999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5521895E-02 -0.3130106 midg,1,midg; midg,igrid,midg 3.1920791E-02 -0.1388695 1,midg,midg; igrid,midg,midg 0.6321760 7.6141126E-02 gauss-seidel spectral radius is 0.9992083 estimated iterations to convergence 281 setup time was (sec) 1.550000 now iterating at: 17:04:34 rms-change max change #iterations 9.530606 284.5741 at 10iterations 5.469131 112.6911 at 20iterations 3.122779 73.21716 at 30iterations 1.778515 36.59964 at 40iterations 1.007719 20.14695 at 50iterations 0.5717517 11.44288 at 60iterations 0.3235129 6.843554 at 70iterations 0.1828692 3.682579 at 80iterations 0.1033909 1.965067 at 90iterations 5.8090568E-02 1.071397 at 100iterations 3.2848317E-02 0.6259379 at 110iterations 1.8540073E-02 0.3759212 at 120iterations 1.0418866E-02 0.2125149 at 130iterations 5.8816979E-03 0.1116056 at 140iterations 3.3139545E-03 6.3677788E-02 at 150iterations 1.8659827E-03 3.7330627E-02 at 160iterations 1.0538052E-03 2.0644665E-02 at 170iterations 5.9502450E-04 1.0898590E-02 at 180iterations finished qdiffx linear iterations at : 17:04:44 total time elapsed so far: 11.13000 # loops : 180 mean,max change (kT/e) : 5.9502450E-04 1.0898590E-02 energy calculations done at 11.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.31000 DelPhi exited at 17:04:45 11.312u 0.181s 0:12.54 91.6% 0+0k 0+0io 0pf+0w