Mon Oct 10 19:43:03 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+sph2.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 = amb2.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 19:43:03 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2385 !!! WARNING: HIR 440 has a net charge of 0.5140 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: 0.6168882 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): 18.63400 65.21700 ymin,ymax (A): 11.80600 55.60100 zmin,zma (A): -1.002000 56.70700 x,y,z range (A): 46.58300 43.79500 57.70900 scale (grids/A): 0.6168882 object centre (A): 41.92550 33.70350 27.85250 number of atom coordinates read : 2385 total number of charged atoms : 2250 net assigned charge : 0.5140053 assigned positive charge : 348.2923 centred at (gu) : 91.27641 89.70464 89.48222 assigned negative charge : -347.7791 centred at (gu) : 91.22752 89.71673 89.49449 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5974 nv = 96 ne = 84 npr = 49149 no. pairs analyzed = 49149 no. exposed pairs = 2968 no. arc points = 21109 no. surface atoms = 1021 nbur = 1364 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 329 mr = 3203 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3072 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2122 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7401 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1186778E-09 -2.9725639E-10 midg,1,midg; midg,igrid,midg 1.0541695E-09 -3.0408512E-10 1,midg,midg; igrid,midg,midg -1.7528421E-09 3.9650256E-09 gauss-seidel spectral radius is 0.9863784 estimated iterations to convergence 70 setup time was (sec) 0.6500000 now iterating at: 19:43:04 rms-change max change #iterations 0.1161103 15.63902 at 10iterations 1.0818563E-02 1.842154 at 20iterations 1.0099098E-03 0.1423569 at 30iterations 9.6776756E-05 1.5548706E-02 at 40iterations 1.0539177E-05 1.6317368E-03 at 50iterations finished qdiffx linear iterations at : 19:43:07 total time elapsed so far: 4.100000 # loops : 50 mean,max change (kT/e) : 1.0539177E-05 1.6317368E-03 energy calculations done at 4.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.280000 DelPhi exited at 19:43:08 4.284u 0.254s 0:04.88 92.8% 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 19:43:08 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2385 !!! WARNING: HIR 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.850665 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): 18.63400 65.21700 ymin,ymax (A): 11.80600 55.60100 zmin,zma (A): -1.002000 56.70700 x,y,z range (A): 46.58300 43.79500 57.70900 scale (grids/A): 1.850665 object centre (A): 41.92550 33.70350 27.85250 number of atom coordinates read : 2385 total number of charged atoms : 2250 net assigned charge : 0.5140053 assigned positive charge : 348.2923 centred at (gu) : 93.82900 89.11338 88.44655 assigned negative charge : -347.7791 centred at (gu) : 93.68282 89.15017 88.48364 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 65841 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21109 grid for indexing accessible points = 1.400000 m= 22734 mr = 45080 m= 3491 mr = 16398 m= 174 mr = 2019 m= 4 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 255 time to turn everything in is 0.5100000 number of dielectric boundary points 28692 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 17649 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) : 0.6168882 object centre at (A) : 41.92550 33.70350 27.85250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8242413E-02 -3.4692120E-02 midg,1,midg; midg,igrid,midg -5.8786850E-03 1.5129361E-03 1,midg,midg; igrid,midg,midg 1.6353711E-02 1.9693634E-02 gauss-seidel spectral radius is 0.9985398 estimated iterations to convergence 207 setup time was (sec) 0.8300000 now iterating at: 19:43:09 rms-change max change #iterations 3.819935 169.4625 at 10iterations 1.733053 64.62879 at 20iterations 0.7957392 30.38538 at 30iterations 0.3620530 13.65692 at 40iterations 0.1656211 5.383392 at 50iterations 7.5666539E-02 2.628969 at 60iterations 3.4542315E-02 1.184340 at 70iterations 1.5727010E-02 0.5423336 at 80iterations 7.1957493E-03 0.2550430 at 90iterations 3.2854055E-03 0.1193438 at 100iterations 1.5023513E-03 4.8741102E-02 at 110iterations 6.8750529E-04 2.3408890E-02 at 120iterations finished qdiffx linear iterations at : 19:43:18 total time elapsed so far: 9.280000 # loops : 120 mean,max change (kT/e) : 6.8750529E-04 2.3408890E-02 energy calculations done at 9.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.450000 DelPhi exited at 19:43:18 9.452u 0.266s 0:10.01 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 Mon Oct 10 2011 at 19:43:18 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2385 !!! WARNING: HIR 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.775997 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): 18.63400 65.21700 ymin,ymax (A): 11.80600 55.60100 zmin,zma (A): -1.002000 56.70700 x,y,z range (A): 46.58300 43.79500 57.70900 scale (grids/A): 2.775997 object centre (A): 41.92550 33.70350 27.85250 number of atom coordinates read : 2385 total number of charged atoms : 2250 net assigned charge : 0.5140053 assigned positive charge : 348.2923 centred at (gu) : 95.74345 88.67011 87.66974 assigned negative charge : -347.7791 centred at (gu) : 95.52425 88.72526 87.72556 start vw surface at 0.1300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 152805 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21109 grid for indexing accessible points = 1.400000 m= 73786 mr = 110039 m= 26402 mr = 59433 m= 5988 mr = 20830 m= 758 mr = 4308 m= 43 mr = 476 m= 0 mr = 9 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 893 time to turn everything in is 1.270000 number of dielectric boundary points 64687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 17997 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) : 1.850665 object centre at (A) : 41.92550 33.70350 27.85250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4568234 -0.4411457 midg,1,midg; midg,igrid,midg -5.0460346E-02 -9.9479975E-03 1,midg,midg; igrid,midg,midg 0.2618187 0.2174150 gauss-seidel spectral radius is 0.9992300 estimated iterations to convergence 284 setup time was (sec) 1.620000 now iterating at: 19:43:20 rms-change max change #iterations 9.118040 310.7029 at 10iterations 5.314481 131.0280 at 20iterations 3.069653 72.18021 at 30iterations 1.768151 36.62387 at 40iterations 1.015231 19.75631 at 50iterations 0.5817008 11.52253 at 60iterations 0.3327719 6.504122 at 70iterations 0.1898122 4.025579 at 80iterations 0.1083266 2.054836 at 90iterations 6.1714374E-02 1.106504 at 100iterations 3.5191111E-02 0.7123699 at 110iterations 2.0039339E-02 0.4531822 at 120iterations 1.1401183E-02 0.2278690 at 130iterations 6.5106442E-03 0.1233973 at 140iterations 3.6983048E-03 7.0721149E-02 at 150iterations 2.1065571E-03 3.9520264E-02 at 160iterations 1.2048052E-03 2.2526652E-02 at 170iterations 6.8979600E-04 1.2695313E-02 at 180iterations finished qdiffx linear iterations at : 19:43:33 total time elapsed so far: 15.02000 # loops : 180 mean,max change (kT/e) : 6.8979600E-04 1.2695313E-02 energy calculations done at 15.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.20000 DelPhi exited at 19:43:34 15.201u 0.287s 0:15.76 98.2% 0+0k 0+0io 0pf+0w