Sat Oct 8 17:26:34 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 17:26:35 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 = 3741 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: 0.5541633 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): -1.893000 60.24400 ymin,ymax (A): -18.44900 44.40100 zmin,zma (A): -5.310000 58.93100 x,y,z range (A): 62.13700 62.85000 64.24100 scale (grids/A): 0.5541633 object centre (A): 29.17550 12.97600 26.81050 number of atom coordinates read : 3741 total number of charged atoms : 3590 net assigned charge : -9.999962 assigned positive charge : 563.1274 centred at (gu) : 88.89754 86.63308 90.43651 assigned negative charge : -573.1298 centred at (gu) : 88.97829 86.65611 90.46973 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7514 nv = 96 ne = 84 npr = 75766 no. pairs analyzed = 75766 no. exposed pairs = 4834 no. arc points = 33913 no. surface atoms = 1612 nbur = 2129 mkacc time = 0.2000000 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 = 1.540000 m= 313 mr = 3902 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3918 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3378 ## 406 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 9788 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3668713E-10 -1.3769860E-09 midg,1,midg; midg,igrid,midg -1.3242138E-09 -5.0907922E-10 1,midg,midg; igrid,midg,midg 8.2468227E-11 -1.3710946E-09 gauss-seidel spectral radius is 0.9832661 estimated iterations to convergence 64 setup time was (sec) 0.7400000 now iterating at: 17:26:36 rms-change max change #iterations 8.7105714E-02 15.14977 at 10iterations 6.2687579E-03 0.9512386 at 20iterations 5.7394936E-04 7.9749584E-02 at 30iterations 1.1755837E-04 2.0977974E-02 at 40iterations 3.4391967E-05 5.8641434E-03 at 50iterations finished qdiffx linear iterations at : 17:26:40 total time elapsed so far: 5.160000 # loops : 50 mean,max change (kT/e) : 3.4391967E-05 5.8641434E-03 energy calculations done at 5.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.340000 DelPhi exited at 17:26:41 5.340u 0.454s 0:06.06 95.5% 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 Sat Oct 8 2011 at 17:26:41 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 = 3741 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: 1.662490 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): -1.893000 60.24400 ymin,ymax (A): -18.44900 44.40100 zmin,zma (A): -5.310000 58.93100 x,y,z range (A): 62.13700 62.85000 64.24100 scale (grids/A): 1.662490 object centre (A): 29.17550 12.97600 26.81050 number of atom coordinates read : 3741 total number of charged atoms : 3590 net assigned charge : -9.999962 assigned positive charge : 563.1274 centred at (gu) : 86.69157 79.89812 91.30851 assigned negative charge : -573.1298 centred at (gu) : 86.93446 79.96777 91.40885 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 82950 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33913 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 26035 mr = 56500 m= 2728 mr = 17603 m= 81 mr = 1218 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.7200000 number of dielectric boundary points 36469 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 351 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 27595 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) : 0.5541633 object centre at (A) : 29.17550 12.97600 26.81050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.7909319E-04 -1.2110007E-02 midg,1,midg; midg,igrid,midg -2.9222596E-02 -9.2083011E-03 1,midg,midg; igrid,midg,midg -1.2417117E-02 -3.5776637E-02 gauss-seidel spectral radius is 0.9983212 estimated iterations to convergence 194 setup time was (sec) 1.140000 now iterating at: 17:26:42 rms-change max change #iterations 3.960915 161.7329 at 10iterations 1.701082 61.20480 at 20iterations 0.7362942 32.69427 at 30iterations 0.3170790 10.23365 at 40iterations 0.1368419 4.878673 at 50iterations 5.8906570E-02 1.850103 at 60iterations 2.5414685E-02 0.7778768 at 70iterations 1.1042778E-02 0.3472366 at 80iterations 4.7745775E-03 0.1683903 at 90iterations 2.0787679E-03 6.9530010E-02 at 100iterations 9.2232740E-04 2.9727936E-02 at 110iterations 4.2069395E-04 1.3468742E-02 at 120iterations finished qdiffx linear iterations at : 17:26:54 total time elapsed so far: 13.36000 # loops : 120 mean,max change (kT/e) : 4.2069395E-04 1.3468742E-02 energy calculations done at 13.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.54000 DelPhi exited at 17:26:55 13.542u 0.529s 0:14.38 97.7% 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 17:26:55 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 = 3741 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: 2.493735 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): -1.893000 60.24400 ymin,ymax (A): -18.44900 44.40100 zmin,zma (A): -5.310000 58.93100 x,y,z range (A): 62.13700 62.85000 64.24100 scale (grids/A): 2.493735 object centre (A): 29.17550 12.97600 26.81050 number of atom coordinates read : 3741 total number of charged atoms : 3590 net assigned charge : -9.999962 assigned positive charge : 563.1274 centred at (gu) : 85.03686 74.84685 91.96249 assigned negative charge : -573.1298 centred at (gu) : 85.40160 74.95151 92.11322 start vw surface at 0.1500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 192675 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33913 grid for indexing accessible points = 1.400000 m= 90009 mr = 138404 m= 25450 mr = 70662 m= 4178 mr = 18660 m= 306 mr = 2497 m= 7 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 1.780000 number of dielectric boundary points 82318 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.950000 number of grid points assigned charge 28692 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) : 1.662490 object centre at (A) : 29.17550 12.97600 26.81050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1335308E-02 2.2818215E-02 midg,1,midg; midg,igrid,midg -0.4398809 -0.1101588 1,midg,midg; igrid,midg,midg -0.1957481 -0.6470417 gauss-seidel spectral radius is 0.9991971 estimated iterations to convergence 279 setup time was (sec) 2.180000 now iterating at: 17:26:58 rms-change max change #iterations 10.16066 350.7861 at 10iterations 5.824973 127.8580 at 20iterations 3.323445 71.95824 at 30iterations 1.886555 37.73651 at 40iterations 1.068941 20.83246 at 50iterations 0.6039805 12.01069 at 60iterations 0.3405840 7.164518 at 70iterations 0.1919388 3.706640 at 80iterations 0.1081746 2.053932 at 90iterations 6.0748391E-02 1.110931 at 100iterations 3.4169223E-02 0.6352634 at 110iterations 1.9225610E-02 0.3479958 at 120iterations 1.0797578E-02 0.1947594 at 130iterations 6.0738693E-03 0.1208944 at 140iterations 3.4177077E-03 6.2752724E-02 at 150iterations 1.9304669E-03 3.6445618E-02 at 160iterations 1.0922076E-03 1.9630432E-02 at 170iterations 6.2009512E-04 1.2280464E-02 at 180iterations finished qdiffx linear iterations at : 17:27:17 total time elapsed so far: 21.58000 # loops : 180 mean,max change (kT/e) : 6.2009512E-04 1.2280464E-02 energy calculations done at 21.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.75000 DelPhi exited at 17:27:18 21.751u 0.584s 0:22.82 97.8% 0+0k 0+0io 0pf+0w