Sat Oct 8 20:37:00 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 Sat Oct 8 2011 at 20:37:00 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2565 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 465 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6256590 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): -31.88200 17.63900 ymin,ymax (A): -23.93900 23.29700 zmin,zma (A): -12.15900 44.74100 x,y,z range (A): 49.52100 47.23600 56.90000 scale (grids/A): 0.6256590 object centre (A): -7.121500 -0.3210001 16.29100 number of atom coordinates read : 2565 total number of charged atoms : 2453 net assigned charge : 3.906008 assigned positive charge : 392.4370 centred at (gu) : 88.50681 89.22601 89.66423 assigned negative charge : -388.5316 centred at (gu) : 88.41757 89.27253 89.56342 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6669 nv = 96 ne = 84 npr = 52294 no. pairs analyzed = 52294 no. exposed pairs = 3034 no. arc points = 21693 no. surface atoms = 1022 nbur = 1543 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 371 mr = 3762 m= 3 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 55 time to turn everything in is 0.3000000 number of dielectric boundary points 3234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2184 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8229 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4492832E-09 1.0803634E-08 midg,1,midg; midg,igrid,midg 8.8266550E-09 1.9307508E-10 1,midg,midg; igrid,midg,midg -4.5574580E-09 7.7730382E-09 gauss-seidel spectral radius is 0.9867642 estimated iterations to convergence 71 setup time was (sec) 0.5400000 now iterating at: 20:37:00 rms-change max change #iterations 0.1338504 17.92208 at 10iterations 1.2737027E-02 1.804085 at 20iterations 1.1824153E-03 0.1748772 at 30iterations 1.1478481E-04 1.7292023E-02 at 40iterations 1.1073973E-05 1.6040802E-03 at 50iterations finished qdiffx linear iterations at : 20:37:03 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.1073973E-05 1.6040802E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 20:37:04 3.364u 0.190s 0:03.84 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 Sat Oct 8 2011 at 20:37:04 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2565 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 465 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.876977 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): -31.88200 17.63900 ymin,ymax (A): -23.93900 23.29700 zmin,zma (A): -12.15900 44.74100 x,y,z range (A): 49.52100 47.23600 56.90000 scale (grids/A): 1.876977 object centre (A): -7.121500 -0.3210001 16.29100 number of atom coordinates read : 2565 total number of charged atoms : 2453 net assigned charge : 3.906008 assigned positive charge : 392.4370 centred at (gu) : 85.51987 87.67776 88.99223 assigned negative charge : -388.5316 centred at (gu) : 85.25240 87.81727 88.69003 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 72471 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21693 grid for indexing accessible points = 1.400000 m= 26329 mr = 50808 m= 3854 mr = 19782 m= 189 mr = 2344 m= 3 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 2585 time to turn everything in is 0.5400000 number of dielectric boundary points 29867 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 19287 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) : 0.6256590 object centre at (A) : -7.121500 -0.3210001 16.29100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3350589E-02 2.3086993E-02 midg,1,midg; midg,igrid,midg 1.3172968E-02 3.3696331E-03 1,midg,midg; igrid,midg,midg -8.3606364E-04 3.1793498E-02 gauss-seidel spectral radius is 0.9985918 estimated iterations to convergence 211 setup time was (sec) 0.8300000 now iterating at: 20:37:05 rms-change max change #iterations 4.112229 203.7905 at 10iterations 1.910880 67.80605 at 20iterations 0.8862399 30.86276 at 30iterations 0.4093046 13.89974 at 40iterations 0.1902156 6.467190 at 50iterations 8.8208780E-02 2.894390 at 60iterations 4.0893413E-02 1.531780 at 70iterations 1.8938446E-02 0.6795664 at 80iterations 8.7793982E-03 0.2797775 at 90iterations 4.0588095E-03 0.1281872 at 100iterations 1.8811543E-03 5.8346748E-02 at 110iterations 8.7153155E-04 3.0316830E-02 at 120iterations finished qdiffx linear iterations at : 20:37:11 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 8.7153155E-04 3.0316830E-02 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.590000 DelPhi exited at 20:37:12 7.594u 0.207s 0:08.08 96.4% 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 8 2011 at 20:37:12 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2565 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 465 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.815466 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): -31.88200 17.63900 ymin,ymax (A): -23.93900 23.29700 zmin,zma (A): -12.15900 44.74100 x,y,z range (A): 49.52100 47.23600 56.90000 scale (grids/A): 2.815466 object centre (A): -7.121500 -0.3210001 16.29100 number of atom coordinates read : 2565 total number of charged atoms : 2453 net assigned charge : 3.906008 assigned positive charge : 392.4370 centred at (gu) : 83.27983 86.51646 88.48814 assigned negative charge : -388.5316 centred at (gu) : 82.87852 86.72585 88.03500 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 167346 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21693 grid for indexing accessible points = 1.400000 m= 86038 mr = 122606 m= 30529 mr = 71413 m= 6834 mr = 24666 m= 838 mr = 5046 m= 45 mr = 525 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.7399999 no. cavity mid-points inaccessible to solvent = 9301 time to turn everything in is 1.300000 number of dielectric boundary points 67358 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 19619 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) : 1.876977 object centre at (A) : -7.121500 -0.3210001 16.29100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4601338E-02 0.2541421 midg,1,midg; midg,igrid,midg 0.1704613 3.3542216E-02 1,midg,midg; igrid,midg,midg 1.2183825E-02 0.4137276 gauss-seidel spectral radius is 0.9992427 estimated iterations to convergence 287 setup time was (sec) 1.610000 now iterating at: 20:37:14 rms-change max change #iterations 9.657640 304.2604 at 10iterations 5.578004 112.3464 at 20iterations 3.195722 62.34524 at 30iterations 1.835349 40.25223 at 40iterations 1.050718 25.27574 at 50iterations 0.6006024 12.37506 at 60iterations 0.3432832 6.227666 at 70iterations 0.1960997 3.493023 at 80iterations 0.1120638 2.476181 at 90iterations 6.3937269E-02 1.179782 at 100iterations 3.6506735E-02 0.7093658 at 110iterations 2.0800529E-02 0.3899264 at 120iterations 1.1891899E-02 0.2127905 at 130iterations 6.7947479E-03 0.1347961 at 140iterations 3.8715843E-03 7.1370602E-02 at 150iterations 2.2145738E-03 4.1038513E-02 at 160iterations 1.2618353E-03 2.3351669E-02 at 170iterations 7.2227337E-04 1.4373779E-02 at 180iterations finished qdiffx linear iterations at : 20:37:24 total time elapsed so far: 11.94000 # loops : 180 mean,max change (kT/e) : 7.2227337E-04 1.4373779E-02 energy calculations done at 11.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.11000 DelPhi exited at 20:37:24 12.117u 0.248s 0:12.64 97.7% 0+0k 0+0io 0pf+0w