Tue Oct 11 06:11:47 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 06:11:47 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 = 2065 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: 0.7210711 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): 3.604000 46.46400 ymin,ymax (A): 0.6409999 41.44200 zmin,zma (A): -2.097000 47.27400 x,y,z range (A): 42.86000 40.80100 49.37100 scale (grids/A): 0.7210711 object centre (A): 25.03400 21.04150 22.58850 number of atom coordinates read : 2065 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 90.30107 90.28127 90.33150 assigned negative charge : -305.3172 centred at (gu) : 90.49671 90.26849 90.38090 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7403 nv = 96 ne = 84 npr = 41405 no. pairs analyzed = 41405 no. exposed pairs = 2509 no. arc points = 17167 no. surface atoms = 852 nbur = 1213 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 531 mr = 4331 m= 5 mr = 85 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 0.2700000 number of dielectric boundary points 3523 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1595 ## 131 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8003 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1235430E-07 5.8480477E-08 midg,1,midg; midg,igrid,midg 7.5181646E-08 1.0096876E-07 1,midg,midg; igrid,midg,midg 2.0078112E-07 -4.5517069E-08 gauss-seidel spectral radius is 0.9899693 estimated iterations to convergence 81 setup time was (sec) 0.4800000 now iterating at: 06:11:48 rms-change max change #iterations 0.2114633 26.94314 at 10iterations 2.8237723E-02 4.412945 at 20iterations 3.9024006E-03 0.5493774 at 30iterations 7.0893206E-04 8.7039948E-02 at 40iterations 1.9587183E-04 2.5539398E-02 at 50iterations finished qdiffx linear iterations at : 06:11:50 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 1.9587183E-04 2.5539398E-02 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 06:11:51 3.061u 0.126s 0:03.55 89.5% 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 06:11:51 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 = 2065 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: 2.163213 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): 3.604000 46.46400 ymin,ymax (A): 0.6409999 41.44200 zmin,zma (A): -2.097000 47.27400 x,y,z range (A): 42.86000 40.80100 49.37100 scale (grids/A): 2.163213 object centre (A): 25.03400 21.04150 22.58850 number of atom coordinates read : 2065 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 90.90317 90.84392 90.99443 assigned negative charge : -305.3172 centred at (gu) : 91.49043 90.80565 91.14260 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 78262 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17167 grid for indexing accessible points = 1.400000 m= 32288 mr = 56087 m= 6358 mr = 24695 m= 569 mr = 4235 m= 15 mr = 267 m= 0 mr = 3 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 32205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 49 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 15367 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) : 0.7210711 object centre at (A) : 25.03400 21.04150 22.58850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7368463E-02 6.1963584E-02 midg,1,midg; midg,igrid,midg 7.7290558E-03 3.3494782E-02 1,midg,midg; igrid,midg,midg 5.0809018E-02 -3.8430430E-03 gauss-seidel spectral radius is 0.9988672 estimated iterations to convergence 235 setup time was (sec) 0.8500000 now iterating at: 06:11:52 rms-change max change #iterations 4.724366 205.2615 at 10iterations 2.369876 84.03800 at 20iterations 1.193638 36.20191 at 30iterations 0.5989317 18.01964 at 40iterations 0.3011482 8.960655 at 50iterations 0.1513178 5.003590 at 60iterations 7.5906098E-02 2.125253 at 70iterations 3.8437448E-02 1.169607 at 80iterations 1.9406270E-02 0.5832057 at 90iterations 9.8795677E-03 0.3061223 at 100iterations 5.0539728E-03 0.1477189 at 110iterations 2.6649926E-03 8.4026337E-02 at 120iterations finished qdiffx linear iterations at : 06:11:59 total time elapsed so far: 7.310000 # loops : 120 mean,max change (kT/e) : 2.6649926E-03 8.4026337E-02 energy calculations done at 7.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.490000 DelPhi exited at 06:11:59 7.489u 0.222s 0:08.02 96.0% 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 06:11:59 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 = 2065 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: 3.244820 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): 3.604000 46.46400 ymin,ymax (A): 0.6409999 41.44200 zmin,zma (A): -2.097000 47.27400 x,y,z range (A): 42.86000 40.80100 49.37100 scale (grids/A): 3.244820 object centre (A): 25.03400 21.04150 22.58850 number of atom coordinates read : 2065 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 91.35483 91.26585 91.49168 assigned negative charge : -305.3172 centred at (gu) : 92.23569 91.20838 91.71387 start vw surface at 0.1300000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 180292 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17167 grid for indexing accessible points = 1.400000 m= 100068 mr = 134794 m= 41345 mr = 83568 m= 12075 mr = 34322 m= 2363 mr = 9372 m= 240 mr = 1651 m= 11 mr = 142 m= 0 mr = 4 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.800000 number of dielectric boundary points 72541 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 15496 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) : 2.163213 object centre at (A) : 25.03400 21.04150 22.58850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5717207 0.6326514 midg,1,midg; midg,igrid,midg 1.2916827E-02 0.2515667 1,midg,midg; igrid,midg,midg 0.3662832 6.4401016E-02 gauss-seidel spectral radius is 0.9993035 estimated iterations to convergence 299 setup time was (sec) 2.110000 now iterating at: 06:12:01 rms-change max change #iterations 10.42010 351.6947 at 10iterations 6.186967 143.8508 at 20iterations 3.659988 72.00615 at 30iterations 2.163936 41.43356 at 40iterations 1.278172 22.62981 at 50iterations 0.7531025 15.51148 at 60iterations 0.4441080 8.080753 at 70iterations 0.2608382 4.568538 at 80iterations 0.1536647 2.672383 at 90iterations 9.0403557E-02 1.558159 at 100iterations 5.3218104E-02 0.9730530 at 110iterations 3.1438965E-02 0.5298347 at 120iterations 1.8678604E-02 0.3088074 at 130iterations 1.1258310E-02 0.1939430 at 140iterations 6.9490434E-03 0.1333275 at 150iterations 4.4573420E-03 7.5649261E-02 at 160iterations 3.0300342E-03 5.4019928E-02 at 170iterations 2.2000247E-03 3.6140442E-02 at 180iterations finished qdiffx linear iterations at : 06:12:12 total time elapsed so far: 12.37000 # loops : 180 mean,max change (kT/e) : 2.2000247E-03 3.6140442E-02 energy calculations done at 12.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 06:12:13 12.556u 0.233s 0:13.78 92.7% 0+0k 0+0io 0pf+0w