Tue Oct 11 04:34:58 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 Tue Oct 11 2011 at 04:34:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2755 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6487708 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): -9.585000 36.70700 ymin,ymax (A): -27.30400 21.47700 zmin,zma (A): -9.107000 45.76600 x,y,z range (A): 46.29200 48.78100 54.87300 scale (grids/A): 0.6487708 object centre (A): 13.56100 -2.913500 18.32950 number of atom coordinates read : 2755 total number of charged atoms : 2632 net assigned charge : 2.500016 assigned positive charge : 420.5286 centred at (gu) : 89.27048 90.75971 91.52190 assigned negative charge : -418.0292 centred at (gu) : 88.99812 90.64845 91.43826 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7958 nv = 96 ne = 84 npr = 54580 no. pairs analyzed = 54580 no. exposed pairs = 3527 no. arc points = 23696 no. surface atoms = 1185 nbur = 1570 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 404 mr = 4519 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3793 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2413 ## 276 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9480 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.1990724E-09 2.4737176E-08 midg,1,midg; midg,igrid,midg -1.1123256E-08 2.6042011E-08 1,midg,midg; igrid,midg,midg -4.6618698E-08 3.9916081E-08 gauss-seidel spectral radius is 0.9877015 estimated iterations to convergence 74 setup time was (sec) 0.3900000 now iterating at: 04:34:59 rms-change max change #iterations 0.1611541 22.36150 at 10iterations 1.6574744E-02 2.200714 at 20iterations 1.7740726E-03 0.2421799 at 30iterations 2.1403830E-04 3.4410477E-02 at 40iterations 3.3416611E-05 4.6539307E-03 at 50iterations finished qdiffx linear iterations at : 04:35:02 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 3.3416611E-05 4.6539307E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 04:35:04 3.388u 0.173s 0:05.80 61.2% 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 04:35:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2755 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.946312 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): -9.585000 36.70700 ymin,ymax (A): -27.30400 21.47700 zmin,zma (A): -9.107000 45.76600 x,y,z range (A): 46.29200 48.78100 54.87300 scale (grids/A): 1.946312 object centre (A): 13.56100 -2.913500 18.32950 number of atom coordinates read : 2755 total number of charged atoms : 2632 net assigned charge : 2.500016 assigned positive charge : 420.5286 centred at (gu) : 87.81085 92.27882 94.56491 assigned negative charge : -418.0292 centred at (gu) : 86.99432 91.94527 94.31437 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 84733 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23696 grid for indexing accessible points = 1.400000 m= 32881 mr = 59929 m= 5402 mr = 24751 m= 317 mr = 3505 m= 3 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 289 time to turn everything in is 0.4100000 number of dielectric boundary points 35043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 159 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 20773 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) : 0.6487708 object centre at (A) : 13.56100 -2.913500 18.32950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5264559E-03 1.0715072E-02 midg,1,midg; midg,igrid,midg -1.1397658E-02 6.7662625E-03 1,midg,midg; igrid,midg,midg -2.8990278E-02 5.1727086E-02 gauss-seidel spectral radius is 0.9987078 estimated iterations to convergence 220 setup time was (sec) 0.6300000 now iterating at: 04:35:05 rms-change max change #iterations 4.608495 178.4431 at 10iterations 2.201202 64.61870 at 20iterations 1.057518 29.42104 at 30iterations 0.5089467 17.41881 at 40iterations 0.2432966 7.580934 at 50iterations 0.1161098 3.276565 at 60iterations 5.5672929E-02 1.631092 at 70iterations 2.6685214E-02 0.8376045 at 80iterations 1.2791887E-02 0.3793068 at 90iterations 6.1559980E-03 0.2043447 at 100iterations 2.9562910E-03 7.9921722E-02 at 110iterations 1.4199793E-03 4.7866821E-02 at 120iterations finished qdiffx linear iterations at : 04:35:12 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 1.4199793E-03 4.7866821E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 04:35:14 7.737u 0.202s 0:09.30 85.2% 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 04:35:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2755 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.919469 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): -9.585000 36.70700 ymin,ymax (A): -27.30400 21.47700 zmin,zma (A): -9.107000 45.76600 x,y,z range (A): 46.29200 48.78100 54.87300 scale (grids/A): 2.919469 object centre (A): 13.56100 -2.913500 18.32950 number of atom coordinates read : 2755 total number of charged atoms : 2632 net assigned charge : 2.500016 assigned positive charge : 420.5286 centred at (gu) : 86.71606 93.41792 96.84727 assigned negative charge : -418.0292 centred at (gu) : 85.49139 92.91777 96.47141 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 195665 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23696 grid for indexing accessible points = 1.400000 m= 104481 mr = 144592 m= 39624 mr = 86616 m= 9896 mr = 32319 m= 1528 mr = 7682 m= 95 mr = 1057 m= 3 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 951 time to turn everything in is 1.090000 number of dielectric boundary points 78986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 21055 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) : 1.946312 object centre at (A) : 13.56100 -2.913500 18.32950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1281798 0.3003695 midg,1,midg; midg,igrid,midg -0.1470187 4.1907582E-02 1,midg,midg; igrid,midg,midg -0.2325484 0.4396785 gauss-seidel spectral radius is 0.9992768 estimated iterations to convergence 293 setup time was (sec) 1.330000 now iterating at: 04:35:15 rms-change max change #iterations 10.73094 371.6523 at 10iterations 6.321362 139.7867 at 20iterations 3.722476 71.55833 at 30iterations 2.179350 40.41875 at 40iterations 1.276195 24.02623 at 50iterations 0.7453600 16.06359 at 60iterations 0.4335240 7.001305 at 70iterations 0.2523752 4.190302 at 80iterations 0.1468340 2.865969 at 90iterations 8.5351303E-02 1.427224 at 100iterations 4.9586773E-02 0.8091259 at 110iterations 2.8851803E-02 0.5052490 at 120iterations 1.6723504E-02 0.3015728 at 130iterations 9.7714160E-03 0.1614418 at 140iterations 5.6936108E-03 0.1040294 at 150iterations 3.3413330E-03 6.8840027E-02 at 160iterations 1.9839753E-03 3.7782669E-02 at 170iterations 1.1925881E-03 2.2100449E-02 at 180iterations finished qdiffx linear iterations at : 04:35:27 total time elapsed so far: 12.64000 # loops : 180 mean,max change (kT/e) : 1.1925881E-03 2.2100449E-02 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.77000 DelPhi exited at 04:35:29 12.778u 0.201s 0:15.04 86.2% 0+0k 0+0io 0pf+0w