Sat Oct 15 13:56:34 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 15 2011 at 13:56:34 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4291 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5110171 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): -15.52400 36.48400 ymin,ymax (A): -30.44800 32.09800 zmin,zma (A): -3.936000 65.72900 x,y,z range (A): 52.00800 62.54600 69.66499 scale (grids/A): 0.5110171 object centre (A): 10.48000 0.8249998 30.89650 number of atom coordinates read : 4291 total number of charged atoms : 4091 net assigned charge : 1.900019 assigned positive charge : 640.0203 centred at (gu) : 90.14511 90.70452 87.34762 assigned negative charge : -638.1243 centred at (gu) : 90.04846 90.74723 87.46399 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7015 nv = 96 ne = 84 npr = 87475 no. pairs analyzed = 87475 no. exposed pairs = 5645 no. arc points = 39741 no. surface atoms = 1882 nbur = 2409 mkacc time = 0.1500000 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 = 1.680000 m= 271 mr = 3474 m= 0 mr = 7 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3863 ## 587 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 9530 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8952282E-10 -1.2715547E-10 midg,1,midg; midg,igrid,midg 9.8888141E-11 -9.7701569E-11 1,midg,midg; igrid,midg,midg -2.0109818E-10 2.5239033E-10 gauss-seidel spectral radius is 0.9803833 estimated iterations to convergence 59 setup time was (sec) 0.5200000 now iterating at: 13:56:35 rms-change max change #iterations 6.4531729E-02 18.29965 at 10iterations 3.6498688E-03 0.6430969 at 20iterations 3.1799538E-04 4.7245026E-02 at 30iterations 8.7891611E-05 1.0591038E-02 at 40iterations 3.1456482E-05 3.8956404E-03 at 50iterations finished qdiffx linear iterations at : 13:56:39 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 3.1456482E-05 3.8956404E-03 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 13:56:39 4.099u 0.265s 0:04.81 90.4% 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 13:56:39 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4291 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.533051 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): -15.52400 36.48400 ymin,ymax (A): -30.44800 32.09800 zmin,zma (A): -3.936000 65.72900 x,y,z range (A): 52.00800 62.54600 69.66499 scale (grids/A): 1.533051 object centre (A): 10.48000 0.8249998 30.89650 number of atom coordinates read : 4291 total number of charged atoms : 4091 net assigned charge : 1.900019 assigned positive charge : 640.0203 centred at (gu) : 90.43406 92.11208 82.04157 assigned negative charge : -638.1243 centred at (gu) : 90.14541 92.24154 82.39177 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 79121 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39741 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 22029 mr = 52853 m= 1911 mr = 13986 m= 39 mr = 766 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 61 time to turn everything in is 0.4100000 number of dielectric boundary points 35495 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 517 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 30853 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) : 0.5110171 object centre at (A) : 10.48000 0.8249998 30.89650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0749093E-03 -1.1197126E-02 midg,1,midg; midg,igrid,midg -1.8263008E-03 -1.1227654E-02 1,midg,midg; igrid,midg,midg -6.2515683E-05 9.3286512E-03 gauss-seidel spectral radius is 0.9980708 estimated iterations to convergence 181 setup time was (sec) 0.6900000 now iterating at: 13:56:40 rms-change max change #iterations 3.567537 140.6233 at 10iterations 1.439611 48.41454 at 20iterations 0.5861551 21.62375 at 30iterations 0.2368460 7.852180 at 40iterations 9.6127346E-02 3.207413 at 50iterations 3.8978770E-02 1.202438 at 60iterations 1.5851088E-02 0.5188074 at 70iterations 6.4526750E-03 0.2076569 at 80iterations 2.6400867E-03 9.4425201E-02 at 90iterations 1.0915881E-03 4.1825533E-02 at 100iterations 4.6213088E-04 1.6395569E-02 at 110iterations 2.0918035E-04 7.0000887E-03 at 120iterations finished qdiffx linear iterations at : 13:56:49 total time elapsed so far: 9.310000 # loops : 120 mean,max change (kT/e) : 2.0918035E-04 7.0000887E-03 energy calculations done at 9.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.440000 DelPhi exited at 13:56:49 9.440u 0.310s 0:10.04 97.1% 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 13:56:49 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4291 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.299577 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): -15.52400 36.48400 ymin,ymax (A): -30.44800 32.09800 zmin,zma (A): -3.936000 65.72900 x,y,z range (A): 52.00800 62.54600 69.66499 scale (grids/A): 2.299577 object centre (A): 10.48000 0.8249998 30.89650 number of atom coordinates read : 4291 total number of charged atoms : 4091 net assigned charge : 1.900019 assigned positive charge : 640.0203 centred at (gu) : 90.65070 93.16795 78.06211 assigned negative charge : -638.1243 centred at (gu) : 90.21796 93.36222 78.58767 start vw surface at 0.1100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 184527 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39741 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 79730 mr = 130396 m= 19499 mr = 60897 m= 2672 mr = 13478 m= 156 mr = 1586 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 243 time to turn everything in is 1.030000 number of dielectric boundary points 80187 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 32632 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) : 1.533051 object centre at (A) : 10.48000 0.8249998 30.89650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1349838 -0.2622961 midg,1,midg; midg,igrid,midg -0.1083121 -0.2668470 1,midg,midg; igrid,midg,midg -7.3886272E-03 0.1528445 gauss-seidel spectral radius is 0.9991398 estimated iterations to convergence 269 setup time was (sec) 1.360000 now iterating at: 13:56:51 rms-change max change #iterations 9.701249 298.3628 at 10iterations 5.538774 128.4359 at 20iterations 3.127902 69.92546 at 30iterations 1.761592 43.89720 at 40iterations 0.9883192 21.76341 at 50iterations 0.5507557 13.26249 at 60iterations 0.3073305 7.166342 at 70iterations 0.1702266 3.798649 at 80iterations 9.4518647E-02 2.089898 at 90iterations 5.2447706E-02 1.100800 at 100iterations 2.8978031E-02 0.6210938 at 110iterations 1.6043203E-02 0.3349819 at 120iterations 8.8796942E-03 0.1821108 at 130iterations 4.9098954E-03 0.1071224 at 140iterations 2.7267782E-03 6.2690735E-02 at 150iterations 1.5206586E-03 2.9436111E-02 at 160iterations 8.5511018E-04 1.6934156E-02 at 170iterations 4.8843742E-04 1.0083199E-02 at 180iterations finished qdiffx linear iterations at : 13:57:06 total time elapsed so far: 16.75000 # loops : 180 mean,max change (kT/e) : 4.8843742E-04 1.0083199E-02 energy calculations done at 16.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.89000 DelPhi exited at 13:57:07 16.890u 0.348s 0:17.55 98.1% 0+0k 0+0io 0pf+0w