Tue Oct 11 03:24:43 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 03:24:43 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: 361 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5575 !!! WARNING: ASL 187 has a net charge of -0.1000 !!! WARNING: HIR 349 has a net charge of 0.5140 !!! WARNING: GLM 837 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4989768 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): -12.42900 50.83700 ymin,ymax (A): -45.44700 25.89900 zmin,zma (A): -14.83700 52.30900 x,y,z range (A): 63.26600 71.34600 67.14600 scale (grids/A): 0.4989768 object centre (A): 19.20400 -9.774001 18.73600 number of atom coordinates read : 5575 total number of charged atoms : 5408 net assigned charge : -0.1799505 assigned positive charge : 868.9586 centred at (gu) : 90.46423 90.26137 88.41425 assigned negative charge : -869.1465 centred at (gu) : 90.48253 90.23679 88.52058 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8818 nv = 96 ne = 84 npr = 109610 no. pairs analyzed = 109610 no. exposed pairs = 7238 no. arc points = 50230 no. surface atoms = 2398 nbur = 3177 mkacc time = 0.2400000 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 = 1.708000 m= 317 mr = 4432 m= 0 mr = 7 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 4696 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4747 ## 671 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 11796 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9972475E-10 -1.3622806E-10 midg,1,midg; midg,igrid,midg -4.8132436E-11 4.4497250E-11 1,midg,midg; igrid,midg,midg 2.6060910E-11 -4.5093297E-11 gauss-seidel spectral radius is 0.9795284 estimated iterations to convergence 58 setup time was (sec) 0.7300000 now iterating at: 03:24:44 rms-change max change #iterations 6.8992965E-02 10.18860 at 10iterations 3.7462630E-03 0.5469208 at 20iterations 3.1970348E-04 5.0865173E-02 at 30iterations 6.5866676E-05 1.2687683E-02 at 40iterations 1.6829172E-05 3.2157898E-03 at 50iterations finished qdiffx linear iterations at : 03:24:47 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 1.6829172E-05 3.2157898E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 03:24:47 3.525u 0.199s 0:04.19 88.5% 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 03:24:48 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: 361 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5575 !!! WARNING: ASL 187 has a net charge of -0.1000 !!! WARNING: HIR 349 has a net charge of 0.5140 !!! WARNING: GLM 837 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.496930 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): -12.42900 50.83700 ymin,ymax (A): -45.44700 25.89900 zmin,zma (A): -14.83700 52.30900 x,y,z range (A): 63.26600 71.34600 67.14600 scale (grids/A): 1.496930 object centre (A): 19.20400 -9.774001 18.73600 number of atom coordinates read : 5575 total number of charged atoms : 5408 net assigned charge : -0.1799505 assigned positive charge : 868.9586 centred at (gu) : 91.39064 90.78214 85.24116 assigned negative charge : -869.1465 centred at (gu) : 91.44731 90.71021 85.56153 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 100505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50230 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 28712 mr = 68248 m= 2254 mr = 18751 m= 46 mr = 840 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1021 time to turn everything in is 0.6900000 number of dielectric boundary points 43678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 585 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 40222 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) : 0.4989768 object centre at (A) : 19.20400 -9.774001 18.73600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2923105E-02 5.1602814E-03 midg,1,midg; midg,igrid,midg -1.2449395E-02 -1.7325945E-02 1,midg,midg; igrid,midg,midg -6.0181506E-04 -4.7266209E-03 gauss-seidel spectral radius is 0.9980924 estimated iterations to convergence 182 setup time was (sec) 0.9800000 now iterating at: 03:24:49 rms-change max change #iterations 4.068757 164.7696 at 10iterations 1.651981 59.95933 at 20iterations 0.6756078 20.64699 at 30iterations 0.2751638 8.557156 at 40iterations 0.1126122 3.742771 at 50iterations 4.5900293E-02 1.350555 at 60iterations 1.8734276E-02 0.6475258 at 70iterations 7.6788878E-03 0.2199650 at 80iterations 3.1496030E-03 0.1110554 at 90iterations 1.2945825E-03 3.7475586E-02 at 100iterations 5.3686183E-04 1.6777039E-02 at 110iterations 2.2546732E-04 7.2391368E-03 at 120iterations finished qdiffx linear iterations at : 03:24:55 total time elapsed so far: 7.410000 # loops : 120 mean,max change (kT/e) : 2.2546732E-04 7.2391368E-03 energy calculations done at 7.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 03:24:56 7.582u 0.226s 0:08.21 95.0% 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 Tue Oct 11 2011 at 03:24:56 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: 361 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5575 !!! WARNING: ASL 187 has a net charge of -0.1000 !!! WARNING: HIR 349 has a net charge of 0.5140 !!! WARNING: GLM 837 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.245396 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): -12.42900 50.83700 ymin,ymax (A): -45.44700 25.89900 zmin,zma (A): -14.83700 52.30900 x,y,z range (A): 63.26600 71.34600 67.14600 scale (grids/A): 2.245396 object centre (A): 19.20400 -9.774001 18.73600 number of atom coordinates read : 5575 total number of charged atoms : 5408 net assigned charge : -0.1799505 assigned positive charge : 868.9586 centred at (gu) : 92.08568 91.17271 82.86090 assigned negative charge : -869.1465 centred at (gu) : 92.17079 91.06519 83.34229 start vw surface at 0.2100000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 234429 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50230 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 104055 mr = 168039 m= 24758 mr = 80545 m= 2956 mr = 17319 m= 122 mr = 1586 m= 0 mr = 24 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 3582 time to turn everything in is 1.670000 number of dielectric boundary points 98807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 88 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 43090 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) : 1.496930 object centre at (A) : 19.20400 -9.774001 18.73600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1896640 0.1318904 midg,1,midg; midg,igrid,midg -0.3144078 -0.4388236 1,midg,midg; igrid,midg,midg 8.7273651E-04 -3.5890445E-02 gauss-seidel spectral radius is 0.9991751 estimated iterations to convergence 275 setup time was (sec) 2.010000 now iterating at: 03:24:58 rms-change max change #iterations 11.24380 263.5747 at 10iterations 6.505832 175.2798 at 20iterations 3.732160 79.33702 at 30iterations 2.132523 43.34624 at 40iterations 1.211169 25.63545 at 50iterations 0.6852772 13.03163 at 60iterations 0.3863440 8.087740 at 70iterations 0.2177694 4.491896 at 80iterations 0.1226853 2.320560 at 90iterations 6.8765365E-02 1.340200 at 100iterations 3.8585000E-02 0.7265129 at 110iterations 2.1638762E-02 0.3994656 at 120iterations 1.2079103E-02 0.2306976 at 130iterations 6.7731552E-03 0.1231499 at 140iterations 3.7830176E-03 7.2122574E-02 at 150iterations 2.1176934E-03 3.9159775E-02 at 160iterations 1.1871455E-03 2.0080566E-02 at 170iterations 6.6446734E-04 1.1476517E-02 at 180iterations finished qdiffx linear iterations at : 03:25:09 total time elapsed so far: 12.89000 # loops : 180 mean,max change (kT/e) : 6.6446734E-04 1.1476517E-02 energy calculations done at 12.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.07000 DelPhi exited at 03:25:09 13.069u 0.207s 0:13.59 97.5% 0+0k 0+0io 0pf+0w