Sat Oct 15 12:24:30 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 15 2011 at 12:24:30 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 = 2342 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6486880 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): -14.93300 39.94700 ymin,ymax (A): -19.26100 25.46700 zmin,zma (A): -5.320000 48.46300 x,y,z range (A): 54.88000 44.72800 53.78300 scale (grids/A): 0.6486880 object centre (A): 12.50700 3.103000 21.57150 number of atom coordinates read : 2342 total number of charged atoms : 2208 net assigned charge : -3.999999 assigned positive charge : 307.4325 centred at (gu) : 91.65208 90.11076 89.84866 assigned negative charge : -311.4330 centred at (gu) : 91.56898 90.14991 90.08263 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7228 nv = 96 ne = 84 npr = 47586 no. pairs analyzed = 47586 no. exposed pairs = 3321 no. arc points = 24910 no. surface atoms = 1108 nbur = 1234 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 493 mr = 3520 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 4153 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2071 ## 119 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8025 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9956305E-08 -3.4778349E-08 midg,1,midg; midg,igrid,midg -2.9511353E-09 -1.2536328E-08 1,midg,midg; igrid,midg,midg -1.2399763E-08 3.2228065E-09 gauss-seidel spectral radius is 0.9876894 estimated iterations to convergence 74 setup time was (sec) 0.3800000 now iterating at: 12:24:31 rms-change max change #iterations 0.1389398 18.97625 at 10iterations 1.4043688E-02 2.090202 at 20iterations 1.4795157E-03 0.2152739 at 30iterations 2.0639360E-04 2.5484085E-02 at 40iterations 4.9576738E-05 6.6251755E-03 at 50iterations finished qdiffx linear iterations at : 12:24:34 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 4.9576738E-05 6.6251755E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 12:24:34 3.444u 0.183s 0:03.92 92.3% 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 15 2011 at 12:24:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2342 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.946064 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): -14.93300 39.94700 ymin,ymax (A): -19.26100 25.46700 zmin,zma (A): -5.320000 48.46300 x,y,z range (A): 54.88000 44.72800 53.78300 scale (grids/A): 1.946064 object centre (A): 12.50700 3.103000 21.57150 number of atom coordinates read : 2342 total number of charged atoms : 2208 net assigned charge : -3.999999 assigned positive charge : 307.4325 centred at (gu) : 94.95584 90.33202 89.54592 assigned negative charge : -311.4330 centred at (gu) : 94.70704 90.44970 90.24796 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 75926 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24910 grid for indexing accessible points = 1.400000 m= 27770 mr = 49235 m= 5484 mr = 18772 m= 419 mr = 3171 m= 8 mr = 150 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 38279 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 17469 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) : 0.6486880 object centre at (A) : 12.50700 3.103000 21.57150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4371878E-02 -5.5043768E-02 midg,1,midg; midg,igrid,midg 4.6110083E-03 2.5218970E-03 1,midg,midg; igrid,midg,midg -6.3635423E-03 8.2234765E-04 gauss-seidel spectral radius is 0.9987062 estimated iterations to convergence 220 setup time was (sec) 0.6200000 now iterating at: 12:24:35 rms-change max change #iterations 3.951854 196.7627 at 10iterations 1.903313 66.66590 at 20iterations 0.9057856 33.61713 at 30iterations 0.4352600 14.40281 at 40iterations 0.2072097 6.255960 at 50iterations 9.9635072E-02 3.652021 at 60iterations 4.7662742E-02 1.681100 at 70iterations 2.2752812E-02 0.7862873 at 80iterations 1.0883866E-02 0.3759804 at 90iterations 5.2084802E-03 0.1614237 at 100iterations 2.5020880E-03 8.1149101E-02 at 110iterations 1.1994228E-03 3.6328316E-02 at 120iterations finished qdiffx linear iterations at : 12:24:42 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 1.1994228E-03 3.6328316E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 12:24:43 8.022u 0.210s 0:08.52 96.5% 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 15 2011 at 12:24:43 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 = 2342 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.919096 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): -14.93300 39.94700 ymin,ymax (A): -19.26100 25.46700 zmin,zma (A): -5.320000 48.46300 x,y,z range (A): 54.88000 44.72800 53.78300 scale (grids/A): 2.919096 object centre (A): 12.50700 3.103000 21.57150 number of atom coordinates read : 2342 total number of charged atoms : 2208 net assigned charge : -3.999999 assigned positive charge : 307.4325 centred at (gu) : 97.43353 90.49809 89.31881 assigned negative charge : -311.4330 centred at (gu) : 97.06055 90.67436 90.37189 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 175579 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24910 grid for indexing accessible points = 1.400000 m= 86019 mr = 120624 m= 34484 mr = 66697 m= 9780 mr = 26006 m= 1656 mr = 6923 m= 122 mr = 1026 m= 2 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9900000 number of dielectric boundary points 86315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 17664 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) : 1.946064 object centre at (A) : 12.50700 3.103000 21.57150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1131591 -0.4228943 midg,1,midg; midg,igrid,midg 2.7421631E-02 4.9746070E-02 1,midg,midg; igrid,midg,midg -3.9198328E-02 2.0358749E-02 gauss-seidel spectral radius is 0.9993058 estimated iterations to convergence 299 setup time was (sec) 1.250000 now iterating at: 12:24:44 rms-change max change #iterations 9.401893 336.1354 at 10iterations 5.638712 127.1118 at 20iterations 3.369013 72.76120 at 30iterations 2.000105 42.96560 at 40iterations 1.183721 25.99893 at 50iterations 0.6996388 14.63125 at 60iterations 0.4123058 7.452236 at 70iterations 0.2426600 4.931208 at 80iterations 0.1426662 2.753643 at 90iterations 8.3823361E-02 1.575336 at 100iterations 4.9094535E-02 0.9675303 at 110iterations 2.8809059E-02 0.5258751 at 120iterations 1.6870700E-02 0.2960625 at 130iterations 9.8803053E-03 0.1738663 at 140iterations 5.7933135E-03 0.1117458 at 150iterations 3.4032618E-03 6.2593460E-02 at 160iterations 1.9917844E-03 3.4726143E-02 at 170iterations 1.1692795E-03 2.0718098E-02 at 180iterations finished qdiffx linear iterations at : 12:24:56 total time elapsed so far: 13.33000 # loops : 180 mean,max change (kT/e) : 1.1692795E-03 2.0718098E-02 energy calculations done at 13.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.46000 DelPhi exited at 12:24:57 13.465u 0.235s 0:14.00 97.7% 0+0k 0+0io 0pf+0w