Sat Jul 18 13:37:28 PDT 2009 #!/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 Jul 18 2009 at 13:37:28 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2803 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: 0.4849079 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.000000 78.00000 ionic strength (M) : 0.1000000 debye length (A) : 9.635460 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): -32.49700 16.01900 ymin,ymax (A): -36.46500 24.60200 zmin,zma (A): 6.813000 80.22900 x,y,z range (A): 48.51600 61.06700 73.41600 scale (grids/A): 0.4849079 object centre (A): -8.239000 -5.931500 43.52100 number of atom coordinates read : 2803 total number of charged atoms : 2697 net assigned charge : 10.50002 assigned positive charge : 405.7417 centred at (gu) : 90.79180 89.09811 86.97765 assigned negative charge : -395.2429 centred at (gu) : 90.86459 89.00288 87.42220 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 4220 nv = 96 ne = 84 npr = 55677 no. pairs analyzed = 55677 no. exposed pairs = 3933 no. arc points = 27776 no. surface atoms = 1325 nbur = 1478 mkacc time = 0.1900000 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 = 1.764000 m= 151 mr = 1829 m= 0 mr = 5 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 2537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2649 ## 408 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 5737 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9957197E-08 -3.2679255E-09 midg,1,midg; midg,igrid,midg 1.7827381E-10 2.9902385E-09 1,midg,midg; igrid,midg,midg 2.7300355E-09 6.8602929E-10 gauss-seidel spectral radius is 0.9847505 estimated iterations to convergence 66 setup time was (sec) 0.7000000 now iterating at: 13:37:29 rms-change max change #iterations 5.8219820E-02 11.41893 at 10iterations 4.7339429E-03 1.032176 at 20iterations 6.0782174E-04 0.1431580 at 30iterations 1.4608270E-04 3.8211823E-02 at 40iterations 4.0555962E-05 1.0692596E-02 at 50iterations finished qdiffx linear iterations at : 13:37:33 total time elapsed so far: 4.240000 # loops : 50 mean,max change (kT/e) : 4.0555962E-05 1.0692596E-02 energy calculations done at 4.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.450000 DelPhi exited at 13:37:34 4.452u 0.593s 0:05.40 93.3% 0+0k 0+45952io 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 Jul 18 2009 at 13:37:34 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2803 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: 1.454724 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.000000 78.00000 ionic strength (M) : 0.1000000 debye length (A) : 9.635460 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): -32.49700 16.01900 ymin,ymax (A): -36.46500 24.60200 zmin,zma (A): 6.813000 80.22900 x,y,z range (A): 48.51600 61.06700 73.41600 scale (grids/A): 1.454724 object centre (A): -8.239000 -5.931500 43.52100 number of atom coordinates read : 2803 total number of charged atoms : 2697 net assigned charge : 10.50002 assigned positive charge : 405.7417 centred at (gu) : 92.37470 87.29362 80.93243 assigned negative charge : -395.2429 centred at (gu) : 92.59374 87.00851 82.26654 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 47589 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27776 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 12172 mr = 29242 m= 935 mr = 7236 m= 18 mr = 276 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 709 time to turn everything in is 0.5500000 number of dielectric boundary points 23961 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 384 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 19925 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) : 0.4849079 object centre at (A) : -8.239000 -5.931500 43.52100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0748530E-02 -1.3018267E-02 midg,1,midg; midg,igrid,midg 2.1480827E-03 6.5269149E-03 1,midg,midg; igrid,midg,midg 4.4689216E-03 2.4730836E-03 gauss-seidel spectral radius is 0.9982674 estimated iterations to convergence 191 setup time was (sec) 0.9100000 now iterating at: 13:37:35 rms-change max change #iterations 2.777252 185.9182 at 10iterations 1.165346 63.34739 at 20iterations 0.4943053 22.41635 at 30iterations 0.2093506 8.751676 at 40iterations 8.8777579E-02 3.978271 at 50iterations 3.7822984E-02 1.633139 at 60iterations 1.6111713E-02 0.7237625 at 70iterations 6.9649345E-03 0.3174421 at 80iterations 3.0630529E-03 0.1523857 at 90iterations 1.4240153E-03 7.2933197E-02 at 100iterations 7.2571717E-04 4.0721893E-02 at 110iterations 4.1063264E-04 2.2663116E-02 at 120iterations finished qdiffx linear iterations at : 13:37:45 total time elapsed so far: 10.53000 # loops : 120 mean,max change (kT/e) : 4.1063264E-04 2.2663116E-02 energy calculations done at 10.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.75000 DelPhi exited at 13:37:46 10.758u 0.704s 0:12.46 91.8% 0+0k 0+45280io 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 Jul 18 2009 at 13:37:46 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2803 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: 2.182086 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.000000 78.00000 ionic strength (M) : 0.1000000 debye length (A) : 9.635460 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): -32.49700 16.01900 ymin,ymax (A): -36.46500 24.60200 zmin,zma (A): 6.813000 80.22900 x,y,z range (A): 48.51600 61.06700 73.41600 scale (grids/A): 2.182086 object centre (A): -8.239000 -5.931500 43.52100 number of atom coordinates read : 2803 total number of charged atoms : 2697 net assigned charge : 10.50002 assigned positive charge : 405.7417 centred at (gu) : 93.56184 85.94043 76.39840 assigned negative charge : -395.2429 centred at (gu) : 93.89063 85.51266 78.39987 start vw surface at 0.1800000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 110790 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27776 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 44220 mr = 73005 m= 10236 mr = 32135 m= 1092 mr = 6742 m= 34 mr = 542 m= 0 mr = 3 time to grow re-entrant surface = 0.7399999 no. cavity mid-points inaccessible to solvent = 2314 time to turn everything in is 1.320000 number of dielectric boundary points 53945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 21490 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) : 1.454724 object centre at (A) : -8.239000 -5.931500 43.52100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7370783 -0.1878508 midg,1,midg; midg,igrid,midg 5.0333119E-04 5.2356247E-02 1,midg,midg; igrid,midg,midg 3.5055827E-02 1.8896746E-02 gauss-seidel spectral radius is 0.9991247 estimated iterations to convergence 267 setup time was (sec) 1.680000 now iterating at: 13:37:48 rms-change max change #iterations 7.213740 236.8988 at 10iterations 3.995712 132.8994 at 20iterations 2.216149 82.23262 at 30iterations 1.225518 38.85910 at 40iterations 0.6720433 18.92670 at 50iterations 0.3686379 9.494198 at 60iterations 0.2018745 5.358354 at 70iterations 0.1105301 3.155085 at 80iterations 6.0438730E-02 1.610874 at 90iterations 3.3056010E-02 0.9640102 at 100iterations 1.8065238E-02 0.5034742 at 110iterations 9.8601254E-03 0.2435551 at 120iterations 5.3878599E-03 0.1304398 at 130iterations 2.9603650E-03 7.3841095E-02 at 140iterations 1.6291833E-03 4.6031952E-02 at 150iterations 9.0649613E-04 2.4299622E-02 at 160iterations 5.1657704E-04 1.3587952E-02 at 170iterations 3.0479749E-04 8.9206696E-03 at 180iterations finished qdiffx linear iterations at : 13:38:03 total time elapsed so far: 16.65000 # loops : 180 mean,max change (kT/e) : 3.0479749E-04 8.9206696E-03 energy calculations done at 16.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.86000 DelPhi exited at 13:38:05 16.860u 0.734s 0:18.73 93.9% 0+0k 0+45272io 0pf+0w