Sat Oct 8 20:13:49 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 Sat Oct 8 2011 at 20:13:49 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 = 2605 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: 0.6228131 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): -31.12900 17.44100 ymin,ymax (A): -23.57300 22.54100 zmin,zma (A): -12.59600 44.56400 x,y,z range (A): 48.57000 46.11400 57.16000 scale (grids/A): 0.6228131 object centre (A): -6.844000 -0.5159998 15.98400 number of atom coordinates read : 2605 total number of charged atoms : 2465 net assigned charge : 4.000004 assigned positive charge : 391.9950 centred at (gu) : 88.49461 89.25577 89.73392 assigned negative charge : -387.9955 centred at (gu) : 88.39014 89.31280 89.61846 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6553 nv = 96 ne = 84 npr = 54637 no. pairs analyzed = 54637 no. exposed pairs = 3049 no. arc points = 21792 no. surface atoms = 1017 nbur = 1588 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 317 mr = 3626 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 141 time to turn everything in is 0.3500000 number of dielectric boundary points 3206 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2162 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8126 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.0836486E-09 1.1144957E-08 midg,1,midg; midg,igrid,midg 9.0620400E-09 -3.9565259E-10 1,midg,midg; igrid,midg,midg -5.6651364E-09 7.9567783E-09 gauss-seidel spectral radius is 0.9866441 estimated iterations to convergence 71 setup time was (sec) 0.6300000 now iterating at: 20:13:50 rms-change max change #iterations 0.1299727 21.34660 at 10iterations 1.1983634E-02 1.748390 at 20iterations 1.1065920E-03 0.1500626 at 30iterations 1.1202973E-04 1.8203735E-02 at 40iterations 1.1811517E-05 2.0961761E-03 at 50iterations finished qdiffx linear iterations at : 20:13:53 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 1.1811517E-05 2.0961761E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 20:13:54 4.179u 0.259s 0:04.72 93.6% 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 8 2011 at 20:13:54 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 = 2605 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: 1.868439 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): -31.12900 17.44100 ymin,ymax (A): -23.57300 22.54100 zmin,zma (A): -12.59600 44.56400 x,y,z range (A): 48.57000 46.11400 57.16000 scale (grids/A): 1.868439 object centre (A): -6.844000 -0.5159998 15.98400 number of atom coordinates read : 2605 total number of charged atoms : 2465 net assigned charge : 4.000004 assigned positive charge : 391.9950 centred at (gu) : 85.48335 87.76685 89.20120 assigned negative charge : -387.9955 centred at (gu) : 85.17023 87.93813 88.85530 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 71039 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21792 grid for indexing accessible points = 1.400000 m= 24599 mr = 49492 m= 3460 mr = 18143 m= 187 mr = 2123 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 6040 time to turn everything in is 0.6300000 number of dielectric boundary points 29471 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 19356 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) : 0.6228131 object centre at (A) : -6.844000 -0.5159998 15.98400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0051802E-02 2.4375238E-02 midg,1,midg; midg,igrid,midg 1.4576081E-02 9.9993299E-04 1,midg,midg; igrid,midg,midg -3.6975471E-03 3.5085145E-02 gauss-seidel spectral radius is 0.9985799 estimated iterations to convergence 210 setup time was (sec) 0.9500000 now iterating at: 20:13:55 rms-change max change #iterations 4.062488 175.6147 at 10iterations 1.874686 66.41338 at 20iterations 0.8670678 31.65639 at 30iterations 0.3994816 14.05506 at 40iterations 0.1846166 5.653090 at 50iterations 8.5112549E-02 3.033112 at 60iterations 3.9423306E-02 1.297390 at 70iterations 1.8126138E-02 0.5654526 at 80iterations 8.3986539E-03 0.2725010 at 90iterations 3.8871916E-03 0.1220036 at 100iterations 1.7949631E-03 6.2755585E-02 at 110iterations 8.2855322E-04 2.8007507E-02 at 120iterations finished qdiffx linear iterations at : 20:14:04 total time elapsed so far: 9.450000 # loops : 120 mean,max change (kT/e) : 8.2855322E-04 2.8007507E-02 energy calculations done at 9.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.640000 DelPhi exited at 20:14:04 9.638u 0.297s 0:10.28 96.4% 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 8 2011 at 20:14:04 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 = 2605 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: 2.802659 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): -31.12900 17.44100 ymin,ymax (A): -23.57300 22.54100 zmin,zma (A): -12.59600 44.56400 x,y,z range (A): 48.57000 46.11400 57.16000 scale (grids/A): 2.802659 object centre (A): -6.844000 -0.5159998 15.98400 number of atom coordinates read : 2605 total number of charged atoms : 2465 net assigned charge : 4.000004 assigned positive charge : 391.9950 centred at (gu) : 83.22488 86.65017 88.80180 assigned negative charge : -387.9955 centred at (gu) : 82.75528 86.90713 88.28284 start vw surface at 0.1600000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 164605 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21792 grid for indexing accessible points = 1.400000 m= 81060 mr = 119987 m= 27528 mr = 66586 m= 6116 mr = 22067 m= 804 mr = 4506 m= 35 mr = 525 m= 0 mr = 10 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 21309 time to turn everything in is 1.590000 number of dielectric boundary points 66467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 19714 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) : 1.868439 object centre at (A) : -6.844000 -0.5159998 15.98400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1337879 0.2883299 midg,1,midg; midg,igrid,midg 0.1607656 -1.6044760E-02 1,midg,midg; igrid,midg,midg -3.8069151E-02 0.4615565 gauss-seidel spectral radius is 0.9992373 estimated iterations to convergence 286 setup time was (sec) 1.920000 now iterating at: 20:14:06 rms-change max change #iterations 9.551820 337.7503 at 10iterations 5.513350 126.7524 at 20iterations 3.166827 73.70969 at 30iterations 1.812971 34.62170 at 40iterations 1.037845 21.38703 at 50iterations 0.5922397 12.11942 at 60iterations 0.3385426 6.272072 at 70iterations 0.1928178 3.700804 at 80iterations 0.1099609 2.112743 at 90iterations 6.2693879E-02 1.199675 at 100iterations 3.5665505E-02 0.6855087 at 110iterations 2.0355506E-02 0.3966484 at 120iterations 1.1598947E-02 0.2108140 at 130iterations 6.5976284E-03 0.1187134 at 140iterations 3.7714113E-03 7.8250885E-02 at 150iterations 2.1478029E-03 3.9164543E-02 at 160iterations 1.2223716E-03 2.1312714E-02 at 170iterations 6.9776038E-04 1.3301849E-02 at 180iterations finished qdiffx linear iterations at : 20:14:20 total time elapsed so far: 15.94000 # loops : 180 mean,max change (kT/e) : 6.9776038E-04 1.3301849E-02 energy calculations done at 15.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.13000 DelPhi exited at 20:14:21 16.133u 0.321s 0:16.73 98.3% 0+0k 0+0io 0pf+0w