Sun Oct 9 22:20:59 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 Sun Oct 9 2011 at 22:20:59 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 = 3152 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: 0.6344680 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): -5.325000 47.61700 ymin,ymax (A): 39.57200 94.07200 zmin,zma (A): 3.361000 59.47100 x,y,z range (A): 52.94200 54.50000 56.11000 scale (grids/A): 0.6344680 object centre (A): 21.14600 66.82200 31.41600 number of atom coordinates read : 3152 total number of charged atoms : 3005 net assigned charge : 5.500019 assigned positive charge : 477.9427 centred at (gu) : 89.49651 90.12097 88.71896 assigned negative charge : -472.4442 centred at (gu) : 89.48424 90.20230 88.63322 start vw surface at 0.1600000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8589 nv = 96 ne = 84 npr = 61610 no. pairs analyzed = 61610 no. exposed pairs = 4099 no. arc points = 29449 no. surface atoms = 1376 nbur = 1776 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 493 mr = 4544 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 46 time to turn everything in is 0.3900000 number of dielectric boundary points 4498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2907 ## 271 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 10406 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.8528137E-09 1.3181422E-08 midg,1,midg; midg,igrid,midg 1.6371803E-08 -3.0911094E-09 1,midg,midg; igrid,midg,midg 6.0940359E-09 7.6319484E-09 gauss-seidel spectral radius is 0.9871904 estimated iterations to convergence 72 setup time was (sec) 0.6700000 now iterating at: 22:21:00 rms-change max change #iterations 0.1574475 25.56869 at 10iterations 1.4976492E-02 2.300114 at 20iterations 1.4857883E-03 0.2110825 at 30iterations 1.4292945E-04 2.2721291E-02 at 40iterations 1.4447952E-05 1.7375946E-03 at 50iterations finished qdiffx linear iterations at : 22:21:03 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 1.4447952E-05 1.7375946E-03 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 22:21:04 4.129u 0.269s 0:04.68 93.5% 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 Sun Oct 9 2011 at 22:21:04 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 = 3152 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: 1.903404 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): -5.325000 47.61700 ymin,ymax (A): 39.57200 94.07200 zmin,zma (A): 3.361000 59.47100 x,y,z range (A): 52.94200 54.50000 56.11000 scale (grids/A): 1.903404 object centre (A): 21.14600 66.82200 31.41600 number of atom coordinates read : 3152 total number of charged atoms : 3005 net assigned charge : 5.500019 assigned positive charge : 477.9427 centred at (gu) : 88.48878 90.36231 86.15636 assigned negative charge : -472.4442 centred at (gu) : 88.45243 90.60638 85.89925 start vw surface at 0.1700000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 93010 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29449 grid for indexing accessible points = 1.400000 m= 31862 mr = 63037 m= 4899 mr = 22539 m= 301 mr = 2844 m= 4 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 2280 time to turn everything in is 0.7900000 number of dielectric boundary points 41564 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 194 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 23603 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) : 0.6344680 object centre at (A) : 21.14600 66.82200 31.41600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6442235E-02 2.6978310E-02 midg,1,midg; midg,igrid,midg 1.5506969E-02 8.7670854E-04 1,midg,midg; igrid,midg,midg -4.2126672E-03 1.7815948E-03 gauss-seidel spectral radius is 0.9987013 estimated iterations to convergence 220 setup time was (sec) 1.100000 now iterating at: 22:21:05 rms-change max change #iterations 4.678076 190.4498 at 10iterations 2.222703 66.24979 at 20iterations 1.061003 31.29550 at 30iterations 0.5035287 14.89817 at 40iterations 0.2405549 6.691040 at 50iterations 0.1144724 3.794888 at 60iterations 5.4380406E-02 1.781674 at 70iterations 2.5958832E-02 0.7792569 at 80iterations 1.2362896E-02 0.3453684 at 90iterations 5.8745206E-03 0.1756468 at 100iterations 2.8135665E-03 8.4499359E-02 at 110iterations 1.3406697E-03 3.9086342E-02 at 120iterations finished qdiffx linear iterations at : 22:21:13 total time elapsed so far: 9.520000 # loops : 120 mean,max change (kT/e) : 1.3406697E-03 3.9086342E-02 energy calculations done at 9.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.700000 DelPhi exited at 22:21:14 9.705u 0.301s 0:10.30 97.0% 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 Sun Oct 9 2011 at 22:21:14 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 = 3152 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: 2.855106 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): -5.325000 47.61700 ymin,ymax (A): 39.57200 94.07200 zmin,zma (A): 3.361000 59.47100 x,y,z range (A): 52.94200 54.50000 56.11000 scale (grids/A): 2.855106 object centre (A): 21.14600 66.82200 31.41600 number of atom coordinates read : 3152 total number of charged atoms : 3005 net assigned charge : 5.500019 assigned positive charge : 477.9427 centred at (gu) : 87.73301 90.54313 84.23421 assigned negative charge : -472.4442 centred at (gu) : 87.67856 90.90963 83.84877 start vw surface at 0.1700000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 215099 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29449 grid for indexing accessible points = 1.400000 m= 104039 mr = 153110 m= 36031 mr = 83410 m= 8470 mr = 27773 m= 1223 mr = 6071 m= 90 mr = 759 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 1.260000 no. cavity mid-points inaccessible to solvent = 7482 time to turn everything in is 2.070000 number of dielectric boundary points 93776 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 24038 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) : 1.903404 object centre at (A) : 21.14600 66.82200 31.41600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3975555 0.2173936 midg,1,midg; midg,igrid,midg 0.2677372 0.1335634 1,midg,midg; igrid,midg,midg -0.2330345 4.5611974E-02 gauss-seidel spectral radius is 0.9992965 estimated iterations to convergence 297 setup time was (sec) 2.390000 now iterating at: 22:21:17 rms-change max change #iterations 11.18961 345.2295 at 10iterations 6.702342 157.0587 at 20iterations 3.981162 86.64268 at 30iterations 2.361706 50.52576 at 40iterations 1.391149 27.86377 at 50iterations 0.8197486 16.72791 at 60iterations 0.4814114 8.628923 at 70iterations 0.2827691 5.234760 at 80iterations 0.1656831 2.722254 at 90iterations 9.6794553E-02 1.759438 at 100iterations 5.6725189E-02 1.029740 at 110iterations 3.3135284E-02 0.5343561 at 120iterations 1.9362617E-02 0.3045521 at 130iterations 1.1310902E-02 0.1866913 at 140iterations 6.6041225E-03 0.1158087 at 150iterations 3.8490447E-03 6.0897589E-02 at 160iterations 2.2508949E-03 3.6055446E-02 at 170iterations 1.3122216E-03 2.1293640E-02 at 180iterations finished qdiffx linear iterations at : 22:21:31 total time elapsed so far: 16.54000 # loops : 180 mean,max change (kT/e) : 1.3122216E-03 2.1293640E-02 energy calculations done at 16.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.72000 DelPhi exited at 22:21:31 16.717u 0.321s 0:17.31 98.3% 0+0k 0+0io 0pf+0w