Sun Oct 9 02:55:22 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 Sun Oct 9 2011 at 02:55:22 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4142 !!! WARNING: HIZ 388 has a net charge of 0.2000 !!! WARNING: HEM 601 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: 0.5398028 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): -2.756000 58.52300 ymin,ymax (A): 0.7950000 66.74500 zmin,zma (A): 169.6080 227.4370 x,y,z range (A): 61.27900 65.95000 57.82901 scale (grids/A): 0.5398028 object centre (A): 27.88350 33.77000 198.5225 number of atom coordinates read : 4142 total number of charged atoms : 3950 net assigned charge : 17.60001 assigned positive charge : 607.9370 centred at (gu) : 89.38570 91.44787 87.74396 assigned negative charge : -590.3411 centred at (gu) : 89.36971 91.40544 87.74653 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7624 nv = 96 ne = 84 npr = 85273 no. pairs analyzed = 85273 no. exposed pairs = 5163 no. arc points = 35838 no. surface atoms = 1757 nbur = 2385 mkacc time = 0.1400000 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 = 1.568000 m= 290 mr = 3918 m= 1 mr = 21 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 0.2800000 number of dielectric boundary points 3976 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3620 ## 464 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 10133 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5042042E-09 4.8253856E-10 midg,1,midg; midg,igrid,midg 3.9199696E-10 1.6282861E-09 1,midg,midg; igrid,midg,midg 8.5218838E-10 8.2335117E-10 gauss-seidel spectral radius is 0.9823971 estimated iterations to convergence 62 setup time was (sec) 0.4700000 now iterating at: 02:55:23 rms-change max change #iterations 7.8503646E-02 11.50083 at 10iterations 6.3423379E-03 0.9608269 at 20iterations 1.0721425E-03 0.1347771 at 30iterations 2.7217000E-04 3.3239365E-02 at 40iterations 7.3123490E-05 9.0866089E-03 at 50iterations finished qdiffx linear iterations at : 02:55:26 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 7.3123490E-05 9.0866089E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 02:55:26 3.500u 0.177s 0:03.97 92.4% 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 Sun Oct 9 2011 at 02:55:26 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4142 !!! WARNING: HIZ 388 has a net charge of 0.2000 !!! WARNING: HEM 601 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: 1.619408 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): -2.756000 58.52300 ymin,ymax (A): 0.7950000 66.74500 zmin,zma (A): 169.6080 227.4370 x,y,z range (A): 61.27900 65.95000 57.82901 scale (grids/A): 1.619408 object centre (A): 27.88350 33.77000 198.5225 number of atom coordinates read : 4142 total number of charged atoms : 3950 net assigned charge : 17.60001 assigned positive charge : 607.9370 centred at (gu) : 88.15560 94.34229 83.23037 assigned negative charge : -590.3411 centred at (gu) : 88.10865 94.21571 83.23927 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 84699 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35838 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 26750 mr = 57722 m= 2947 mr = 18451 m= 83 mr = 1436 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 36867 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 402 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 30126 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) : 0.5398028 object centre at (A) : 27.88350 33.77000 198.5225 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6018145E-02 5.7530450E-04 midg,1,midg; midg,igrid,midg 1.8613240E-02 3.6790296E-02 1,midg,midg; igrid,midg,midg 3.3752624E-02 8.3566159E-03 gauss-seidel spectral radius is 0.9982723 estimated iterations to convergence 191 setup time was (sec) 0.6400000 now iterating at: 02:55:27 rms-change max change #iterations 3.874536 210.0357 at 10iterations 1.645438 60.18839 at 20iterations 0.6978939 23.52180 at 30iterations 0.2985429 9.515442 at 40iterations 0.1271657 4.148754 at 50iterations 5.4535177E-02 1.769408 at 60iterations 2.3406591E-02 0.8000050 at 70iterations 1.0151468E-02 0.3054867 at 80iterations 4.4961362E-03 0.1453400 at 90iterations 2.0837223E-03 7.6995850E-02 at 100iterations 1.0336811E-03 3.7649155E-02 at 110iterations 5.6754070E-04 2.0460129E-02 at 120iterations finished qdiffx linear iterations at : 02:55:34 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 5.6754070E-04 2.0460129E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 02:55:35 7.930u 0.212s 0:08.40 96.9% 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 Sun Oct 9 2011 at 02:55:35 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4142 !!! WARNING: HIZ 388 has a net charge of 0.2000 !!! WARNING: HEM 601 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: 2.429113 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): -2.756000 58.52300 ymin,ymax (A): 0.7950000 66.74500 zmin,zma (A): 169.6080 227.4370 x,y,z range (A): 61.27900 65.95000 57.82901 scale (grids/A): 2.429113 object centre (A): 27.88350 33.77000 198.5225 number of atom coordinates read : 4142 total number of charged atoms : 3950 net assigned charge : 17.60001 assigned positive charge : 607.9370 centred at (gu) : 87.23296 96.51285 79.84525 assigned negative charge : -590.3411 centred at (gu) : 87.16285 96.32358 79.85890 start vw surface at 0.1100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 196758 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35838 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 91732 mr = 141429 m= 27531 mr = 72414 m= 4664 mr = 20880 m= 324 mr = 3015 m= 4 mr = 129 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.030000 number of dielectric boundary points 83146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 31549 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) : 1.619408 object centre at (A) : 27.88350 33.77000 198.5225 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1755431 -4.2834055E-02 midg,1,midg; midg,igrid,midg 0.2910196 0.6954718 1,midg,midg; igrid,midg,midg 0.4183978 -1.7651537E-02 gauss-seidel spectral radius is 0.9991940 estimated iterations to convergence 278 setup time was (sec) 1.280000 now iterating at: 02:55:36 rms-change max change #iterations 10.01126 291.8497 at 10iterations 5.744497 126.0102 at 20iterations 3.287286 68.16718 at 30iterations 1.867814 41.57669 at 40iterations 1.061113 22.07491 at 50iterations 0.6006485 11.19213 at 60iterations 0.3390974 6.404072 at 70iterations 0.1914466 3.526371 at 80iterations 0.1077897 2.177197 at 90iterations 6.0551196E-02 1.132538 at 100iterations 3.4124658E-02 0.6103458 at 110iterations 1.9202642E-02 0.3701477 at 120iterations 1.0794609E-02 0.2095871 at 130iterations 6.0896194E-03 0.1076088 at 140iterations 3.4417885E-03 6.6439629E-02 at 150iterations 1.9632806E-03 3.6087036E-02 at 160iterations 1.1327399E-03 2.1024704E-02 at 170iterations 6.6449784E-04 1.2926102E-02 at 180iterations finished qdiffx linear iterations at : 02:55:47 total time elapsed so far: 12.71000 # loops : 180 mean,max change (kT/e) : 6.6449784E-04 1.2926102E-02 energy calculations done at 12.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.84000 DelPhi exited at 02:55:48 12.847u 0.200s 0:13.31 97.9% 0+0k 0+0io 0pf+0w