Mon Oct 10 16:58:48 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 16:58:48 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 = 2868 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5667797 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): -34.62800 19.36800 ymin,ymax (A): -13.95800 29.88100 zmin,zma (A): 10.73200 73.54300 x,y,z range (A): 53.99600 43.83900 62.81100 scale (grids/A): 0.5667797 object centre (A): -7.630001 7.961501 42.13750 number of atom coordinates read : 2868 total number of charged atoms : 2727 net assigned charge : 1.500021 assigned positive charge : 425.1776 centred at (gu) : 90.01183 90.37617 89.95433 assigned negative charge : -423.6784 centred at (gu) : 90.02585 90.24848 89.93042 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5993 nv = 96 ne = 84 npr = 58146 no. pairs analyzed = 58146 no. exposed pairs = 3512 no. arc points = 24884 no. surface atoms = 1195 nbur = 1673 mkacc time = 0.1300000 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 = 1.512000 m= 224 mr = 3149 m= 0 mr = 28 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2500 ## 286 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7710 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2410586E-10 5.1315585E-10 midg,1,midg; midg,igrid,midg -1.4050775E-09 2.0655473E-09 1,midg,midg; igrid,midg,midg 3.8558362E-10 1.0722302E-11 gauss-seidel spectral radius is 0.9839290 estimated iterations to convergence 65 setup time was (sec) 0.5800000 now iterating at: 16:58:49 rms-change max change #iterations 8.6986788E-02 16.98230 at 10iterations 6.4378786E-03 0.9515905 at 20iterations 4.8094749E-04 8.5887909E-02 at 30iterations 3.9212035E-05 6.6852570E-03 at 40iterations 4.8116749E-06 1.1978149E-03 at 50iterations finished qdiffx linear iterations at : 16:58:52 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 4.8116749E-06 1.1978149E-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) 4.170000 DelPhi exited at 16:58:53 4.174u 0.234s 0:04.75 92.6% 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 Mon Oct 10 2011 at 16:58:53 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 = 2868 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.700339 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): -34.62800 19.36800 ymin,ymax (A): -13.95800 29.88100 zmin,zma (A): 10.73200 73.54300 x,y,z range (A): 53.99600 43.83900 62.81100 scale (grids/A): 1.700339 object centre (A): -7.630001 7.961501 42.13750 number of atom coordinates read : 2868 total number of charged atoms : 2727 net assigned charge : 1.500021 assigned positive charge : 425.1776 centred at (gu) : 90.03466 91.12784 89.86205 assigned negative charge : -423.6784 centred at (gu) : 90.07743 90.74524 89.79102 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 65603 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24884 grid for indexing accessible points = 1.400000 m= 20724 mr = 44555 m= 2457 mr = 14659 m= 93 mr = 1457 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 3252 time to turn everything in is 0.5700000 number of dielectric boundary points 28180 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 257 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 21093 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) : 0.5667797 object centre at (A) : -7.630001 7.961501 42.13750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3561958E-02 1.9667041E-03 midg,1,midg; midg,igrid,midg -2.3092947E-03 1.1794764E-02 1,midg,midg; igrid,midg,midg 5.7632411E-03 -1.0953994E-03 gauss-seidel spectral radius is 0.9983193 estimated iterations to convergence 194 setup time was (sec) 0.9000000 now iterating at: 16:58:54 rms-change max change #iterations 3.525256 167.5230 at 10iterations 1.511122 65.39580 at 20iterations 0.6472316 25.84345 at 30iterations 0.2792198 10.24829 at 40iterations 0.1200949 4.042988 at 50iterations 5.2068699E-02 1.886635 at 60iterations 2.2298459E-02 0.8127699 at 70iterations 9.6118981E-03 0.3753719 at 80iterations 4.1617099E-03 0.1423564 at 90iterations 1.7919251E-03 5.9584618E-02 at 100iterations 7.7377894E-04 3.4921646E-02 at 110iterations 3.3444894E-04 1.1664391E-02 at 120iterations finished qdiffx linear iterations at : 16:59:02 total time elapsed so far: 9.300000 # loops : 120 mean,max change (kT/e) : 3.3444894E-04 1.1664391E-02 energy calculations done at 9.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.480000 DelPhi exited at 16:59:03 9.485u 0.265s 0:10.37 93.9% 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 16:59:03 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 = 2868 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: 2.550509 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): -34.62800 19.36800 ymin,ymax (A): -13.95800 29.88100 zmin,zma (A): 10.73200 73.54300 x,y,z range (A): 53.99600 43.83900 62.81100 scale (grids/A): 2.550509 object centre (A): -7.630001 7.961501 42.13750 number of atom coordinates read : 2868 total number of charged atoms : 2727 net assigned charge : 1.500021 assigned positive charge : 425.1776 centred at (gu) : 90.05177 91.69157 89.79282 assigned negative charge : -423.6784 centred at (gu) : 90.11612 91.11782 89.68645 start vw surface at 0.1800000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 152326 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24884 grid for indexing accessible points = 1.400000 m= 70639 mr = 108798 m= 21647 mr = 56774 m= 4120 mr = 16642 m= 422 mr = 3049 m= 9 mr = 243 m= 0 mr = 3 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 10688 time to turn everything in is 1.360000 number of dielectric boundary points 63654 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 21807 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) : 1.700339 object centre at (A) : -7.630001 7.961501 42.13750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2453213 8.5743122E-02 midg,1,midg; midg,igrid,midg -3.0185448E-02 0.1288691 1,midg,midg; igrid,midg,midg 5.5054996E-02 5.7435781E-02 gauss-seidel spectral radius is 0.9991763 estimated iterations to convergence 275 setup time was (sec) 1.700000 now iterating at: 16:59:05 rms-change max change #iterations 8.827796 343.9214 at 10iterations 4.977035 137.0257 at 20iterations 2.790905 66.21994 at 30iterations 1.565062 36.09524 at 40iterations 0.8750124 19.00038 at 50iterations 0.4892482 10.01250 at 60iterations 0.2732198 5.666720 at 70iterations 0.1524215 3.119217 at 80iterations 8.4670991E-02 1.663098 at 90iterations 4.7201380E-02 1.059057 at 100iterations 2.6317246E-02 0.5103092 at 110iterations 1.4649850E-02 0.3220835 at 120iterations 8.1584519E-03 0.1652069 at 130iterations 4.5403223E-03 9.7885132E-02 at 140iterations 2.5271140E-03 4.9606323E-02 at 150iterations 1.4065854E-03 2.5936127E-02 at 160iterations 7.8269711E-04 1.5849590E-02 at 170iterations 4.3570463E-04 8.3541870E-03 at 180iterations finished qdiffx linear iterations at : 16:59:19 total time elapsed so far: 15.14000 # loops : 180 mean,max change (kT/e) : 4.3570463E-04 8.3541870E-03 energy calculations done at 15.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.34000 DelPhi exited at 16:59:21 15.345u 0.276s 0:17.47 89.3% 0+0k 0+0io 0pf+0w