Tue Oct 11 03:21:39 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 Tue Oct 11 2011 at 03:21:39 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2966 !!! WARNING: HIR 128 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: 0.5936895 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): -22.86900 30.86500 ymin,ymax (A): 8.556000 68.52000 zmin,zma (A): -24.78500 32.16400 x,y,z range (A): 53.73400 59.96400 56.94900 scale (grids/A): 0.5936895 object centre (A): 3.998000 38.53800 3.689501 number of atom coordinates read : 2966 total number of charged atoms : 2812 net assigned charge : -5.985987 assigned positive charge : 439.5302 centred at (gu) : 90.81531 87.87723 87.26185 assigned negative charge : -445.5174 centred at (gu) : 90.83356 87.85762 87.26340 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7156 nv = 96 ne = 84 npr = 57152 no. pairs analyzed = 57152 no. exposed pairs = 4261 no. arc points = 29999 no. surface atoms = 1410 nbur = 1556 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 371 mr = 3515 m= 0 mr = 17 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3995 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2984 ## 308 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8868 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6643686E-09 -1.1472889E-09 midg,1,midg; midg,igrid,midg -4.3709321E-09 -8.7170510E-10 1,midg,midg; igrid,midg,midg -1.1883121E-09 -3.1866605E-09 gauss-seidel spectral radius is 0.9853648 estimated iterations to convergence 68 setup time was (sec) 0.4000000 now iterating at: 03:21:40 rms-change max change #iterations 0.1113785 16.90862 at 10iterations 9.1288975E-03 1.294810 at 20iterations 7.4538519E-04 0.1157541 at 30iterations 6.2870604E-05 9.5634460E-03 at 40iterations 5.6441831E-06 8.3541870E-04 at 50iterations finished qdiffx linear iterations at : 03:21:43 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 5.6441831E-06 8.3541870E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 03:21:43 3.442u 0.174s 0:03.90 92.5% 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 Tue Oct 11 2011 at 03:21:43 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2966 !!! WARNING: HIR 128 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: 1.781069 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): -22.86900 30.86500 ymin,ymax (A): 8.556000 68.52000 zmin,zma (A): -24.78500 32.16400 x,y,z range (A): 53.73400 59.96400 56.94900 scale (grids/A): 1.781069 object centre (A): 3.998000 38.53800 3.689501 number of atom coordinates read : 2966 total number of charged atoms : 2812 net assigned charge : -5.985987 assigned positive charge : 439.5302 centred at (gu) : 92.44495 83.63073 81.78478 assigned negative charge : -445.5174 centred at (gu) : 92.50063 83.57260 81.79011 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 77399 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29999 grid for indexing accessible points = 1.400000 m= 25988 mr = 50459 m= 3263 mr = 17804 m= 127 mr = 1652 m= 0 mr = 17 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 36845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 222 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 21875 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) : 0.5936895 object centre at (A) : 3.998000 38.53800 3.689501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2650908E-03 -3.0596700E-02 midg,1,midg; midg,igrid,midg -4.3375608E-02 -2.6380727E-02 1,midg,midg; igrid,midg,midg 1.5543328E-03 -6.6240025E-03 gauss-seidel spectral radius is 0.9984919 estimated iterations to convergence 204 setup time was (sec) 0.6100000 now iterating at: 03:21:44 rms-change max change #iterations 4.014117 176.9316 at 10iterations 1.799706 65.50791 at 20iterations 0.8099537 24.45330 at 30iterations 0.3650573 11.94238 at 40iterations 0.1636041 5.275139 at 50iterations 7.3664084E-02 2.502171 at 60iterations 3.3094928E-02 1.157362 at 70iterations 1.4879161E-02 0.4681091 at 80iterations 6.7347260E-03 0.2138143 at 90iterations 3.0180630E-03 0.1052456 at 100iterations 1.3571155E-03 4.0494442E-02 at 110iterations 6.1264850E-04 1.9745827E-02 at 120iterations finished qdiffx linear iterations at : 03:21:51 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 6.1264850E-04 1.9745827E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 03:21:52 7.908u 0.207s 0:08.49 95.4% 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 Tue Oct 11 2011 at 03:21:52 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2966 !!! WARNING: HIR 128 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: 2.671603 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): -22.86900 30.86500 ymin,ymax (A): 8.556000 68.52000 zmin,zma (A): -24.78500 32.16400 x,y,z range (A): 53.73400 59.96400 56.94900 scale (grids/A): 2.671603 object centre (A): 3.998000 38.53800 3.689501 number of atom coordinates read : 2966 total number of charged atoms : 2812 net assigned charge : -5.985987 assigned positive charge : 439.5302 centred at (gu) : 93.66702 80.44599 77.67703 assigned negative charge : -445.5174 centred at (gu) : 93.75076 80.35886 77.68496 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 179175 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29999 grid for indexing accessible points = 1.400000 m= 85270 mr = 123530 m= 27937 mr = 66841 m= 5321 mr = 21012 m= 557 mr = 3591 m= 21 mr = 281 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9800000 number of dielectric boundary points 83026 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 22491 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) : 1.781069 object centre at (A) : 3.998000 38.53800 3.689501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1015831 -0.6869087 midg,1,midg; midg,igrid,midg -0.2970086 -0.4601378 1,midg,midg; igrid,midg,midg -4.1887560E-03 -8.2687572E-02 gauss-seidel spectral radius is 0.9992433 estimated iterations to convergence 287 setup time was (sec) 1.230000 now iterating at: 03:21:53 rms-change max change #iterations 9.984724 343.8944 at 10iterations 5.890968 144.2865 at 20iterations 3.433453 70.53615 at 30iterations 1.990640 46.31498 at 40iterations 1.152417 26.09447 at 50iterations 0.6641853 13.09971 at 60iterations 0.3820949 8.034018 at 70iterations 0.2196658 4.015213 at 80iterations 0.1257163 2.273053 at 90iterations 7.1949929E-02 1.528191 at 100iterations 4.1228071E-02 0.7996464 at 110iterations 2.3538604E-02 0.4310713 at 120iterations 1.3477044E-02 0.2335796 at 130iterations 7.6962942E-03 0.1393585 at 140iterations 4.4026431E-03 8.4515572E-02 at 150iterations 2.5210564E-03 4.5046806E-02 at 160iterations 1.4363108E-03 2.5732040E-02 at 170iterations 8.2114147E-04 1.4270782E-02 at 180iterations finished qdiffx linear iterations at : 03:22:05 total time elapsed so far: 12.78000 # loops : 180 mean,max change (kT/e) : 8.2114147E-04 1.4270782E-02 energy calculations done at 12.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.93000 DelPhi exited at 03:22:05 12.930u 0.198s 0:13.47 97.4% 0+0k 0+0io 0pf+0w