Mon Oct 10 00:13:04 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 00:13:04 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 = 3088 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: 0.6291087 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): -19.55600 34.84600 ymin,ymax (A): -38.01900 13.11400 zmin,zma (A): -14.36100 42.22700 x,y,z range (A): 54.40200 51.13300 56.58800 scale (grids/A): 0.6291087 object centre (A): 7.645000 -12.45250 13.93300 number of atom coordinates read : 3088 total number of charged atoms : 2946 net assigned charge : 2.500006 assigned positive charge : 465.1339 centred at (gu) : 89.04855 89.58775 91.60467 assigned negative charge : -462.6353 centred at (gu) : 89.06770 89.68901 91.57117 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8148 nv = 96 ne = 84 npr = 61379 no. pairs analyzed = 61379 no. exposed pairs = 4032 no. arc points = 28515 no. surface atoms = 1344 nbur = 1744 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 390 mr = 4250 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.3600000 number of dielectric boundary points 4256 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2887 ## 284 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 10043 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2042399E-10 8.4232026E-09 midg,1,midg; midg,igrid,midg 1.3983094E-08 -7.2727944E-09 1,midg,midg; igrid,midg,midg 5.4902038E-09 4.6683657E-10 gauss-seidel spectral radius is 0.9869615 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 00:13:05 rms-change max change #iterations 0.1431711 22.06507 at 10iterations 1.3722727E-02 2.112160 at 20iterations 1.2935058E-03 0.1559763 at 30iterations 1.2690555E-04 1.9943237E-02 at 40iterations 1.3253310E-05 1.7700195E-03 at 50iterations finished qdiffx linear iterations at : 00:13:08 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.3253310E-05 1.7700195E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 00:13:08 3.433u 0.139s 0:03.85 92.4% 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 Mon Oct 10 2011 at 00:13:08 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 = 3088 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: 1.887326 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): -19.55600 34.84600 ymin,ymax (A): -38.01900 13.11400 zmin,zma (A): -14.36100 42.22700 x,y,z range (A): 54.40200 51.13300 56.58800 scale (grids/A): 1.887326 object centre (A): 7.645000 -12.45250 13.93300 number of atom coordinates read : 3088 total number of charged atoms : 2946 net assigned charge : 2.500006 assigned positive charge : 465.1339 centred at (gu) : 87.14494 88.76236 94.81320 assigned negative charge : -462.6353 centred at (gu) : 87.20280 89.06659 94.71341 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 88925 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28515 grid for indexing accessible points = 1.400000 m= 29378 mr = 60269 m= 4010 mr = 20695 m= 209 mr = 2272 m= 3 mr = 43 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 2150 time to turn everything in is 0.6300000 number of dielectric boundary points 39247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 192 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 23179 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) : 0.6291087 object centre at (A) : 7.645000 -12.45250 13.93300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2819652E-02 2.7949773E-03 midg,1,midg; midg,igrid,midg 1.5909014E-02 -3.5291410E-03 1,midg,midg; igrid,midg,midg 7.3226546E-03 -1.4406074E-02 gauss-seidel spectral radius is 0.9986682 estimated iterations to convergence 217 setup time was (sec) 0.9200000 now iterating at: 00:13:09 rms-change max change #iterations 4.609928 184.7860 at 10iterations 2.169061 67.78929 at 20iterations 1.021410 35.99180 at 30iterations 0.4832607 14.57079 at 40iterations 0.2283941 6.791592 at 50iterations 0.1077732 3.230640 at 60iterations 5.0800588E-02 1.510140 at 70iterations 2.4053369E-02 0.7391090 at 80iterations 1.1308189E-02 0.3409855 at 90iterations 5.3710956E-03 0.1592016 at 100iterations 2.5307392E-03 8.0528259E-02 at 110iterations 1.1979475E-03 3.3442497E-02 at 120iterations finished qdiffx linear iterations at : 00:13:17 total time elapsed so far: 8.550000 # loops : 120 mean,max change (kT/e) : 1.1979475E-03 3.3442497E-02 energy calculations done at 8.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.770000 DelPhi exited at 00:13:17 8.777u 0.158s 0:09.24 96.5% 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 00:13:18 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 = 3088 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: 2.830989 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): -19.55600 34.84600 ymin,ymax (A): -38.01900 13.11400 zmin,zma (A): -14.36100 42.22700 x,y,z range (A): 54.40200 51.13300 56.58800 scale (grids/A): 2.830989 object centre (A): 7.645000 -12.45250 13.93300 number of atom coordinates read : 3088 total number of charged atoms : 2946 net assigned charge : 2.500006 assigned positive charge : 465.1339 centred at (gu) : 85.71730 88.14346 97.21981 assigned negative charge : -462.6353 centred at (gu) : 85.80410 88.59985 97.07012 start vw surface at 0.1700000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 205963 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28515 grid for indexing accessible points = 1.400000 m= 98007 mr = 146993 m= 32026 mr = 78381 m= 6931 mr = 24655 m= 861 mr = 4854 m= 34 mr = 500 m= 0 mr = 2 time to grow re-entrant surface = 0.9300001 no. cavity mid-points inaccessible to solvent = 6869 time to turn everything in is 1.590000 number of dielectric boundary points 88437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 23566 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) : 1.887326 object centre at (A) : 7.645000 -12.45250 13.93300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1449984 -5.0242368E-02 midg,1,midg; midg,igrid,midg -5.2624688E-02 4.6654720E-02 1,midg,midg; igrid,midg,midg -2.5133912E-02 -0.2719197 gauss-seidel spectral radius is 0.9992913 estimated iterations to convergence 296 setup time was (sec) 1.880000 now iterating at: 00:13:20 rms-change max change #iterations 11.04811 431.4043 at 10iterations 6.658008 143.9959 at 20iterations 3.969822 87.93082 at 30iterations 2.349094 46.63697 at 40iterations 1.387917 25.93140 at 50iterations 0.8155376 14.22506 at 60iterations 0.4791114 8.391114 at 70iterations 0.2802499 4.963917 at 80iterations 0.1637356 3.026444 at 90iterations 9.5549226E-02 1.594201 at 100iterations 5.5733006E-02 0.9843383 at 110iterations 3.2504454E-02 0.5608938 at 120iterations 1.8948354E-02 0.3043365 at 130iterations 1.1036974E-02 0.1940451 at 140iterations 6.4326297E-03 0.1140060 at 150iterations 3.7457417E-03 6.2337875E-02 at 160iterations 2.1826788E-03 3.5583496E-02 at 170iterations 1.2658264E-03 2.3542766E-02 at 180iterations finished qdiffx linear iterations at : 00:13:30 total time elapsed so far: 12.07000 # loops : 180 mean,max change (kT/e) : 1.2658264E-03 2.3542766E-02 energy calculations done at 12.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.26000 DelPhi exited at 00:13:30 12.267u 0.171s 0:12.71 97.7% 0+0k 0+0io 0pf+0w