Sun Oct 9 13:37:52 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 Sun Oct 9 2011 at 13:37:52 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2339 !!! WARNING: GLM 182 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7059290 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): -18.51800 30.39000 ymin,ymax (A): -20.71400 29.71600 zmin,zma (A): 4.075000 48.01100 x,y,z range (A): 48.90800 50.43000 43.93600 scale (grids/A): 0.7059290 object centre (A): 5.936000 4.500999 26.04300 number of atom coordinates read : 2339 total number of charged atoms : 2195 net assigned charge : 3.406011 assigned positive charge : 355.4073 centred at (gu) : 90.64017 90.32968 90.34301 assigned negative charge : -352.0016 centred at (gu) : 90.71191 90.48421 90.48098 start vw surface at 0.1100000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7957 nv = 96 ne = 84 npr = 47225 no. pairs analyzed = 47225 no. exposed pairs = 2954 no. arc points = 20415 no. surface atoms = 1001 nbur = 1338 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 499 mr = 4407 m= 2 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 52 time to turn everything in is 0.2900000 number of dielectric boundary points 3972 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1959 ## 206 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8850 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.5442978E-08 -5.0131618E-08 midg,1,midg; midg,igrid,midg 1.0380872E-07 -5.9811342E-08 1,midg,midg; igrid,midg,midg 5.9274996E-08 -1.1864280E-08 gauss-seidel spectral radius is 0.9895689 estimated iterations to convergence 80 setup time was (sec) 0.5800000 now iterating at: 13:37:53 rms-change max change #iterations 0.2116670 27.20256 at 10iterations 2.6535323E-02 3.768661 at 20iterations 4.0118494E-03 0.6097069 at 30iterations 9.9234260E-04 0.1572037 at 40iterations 3.5592326E-04 5.8734894E-02 at 50iterations finished qdiffx linear iterations at : 13:37:58 total time elapsed so far: 4.830000 # loops : 50 mean,max change (kT/e) : 3.5592326E-04 5.8734894E-02 energy calculations done at 4.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.000000 DelPhi exited at 13:37:58 5.004u 0.445s 0:05.76 94.4% 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 13:37:58 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2339 !!! WARNING: GLM 182 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.117787 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): -18.51800 30.39000 ymin,ymax (A): -20.71400 29.71600 zmin,zma (A): 4.075000 48.01100 x,y,z range (A): 48.90800 50.43000 43.93600 scale (grids/A): 2.117787 object centre (A): 5.936000 4.500999 26.04300 number of atom coordinates read : 2339 total number of charged atoms : 2195 net assigned charge : 3.406011 assigned positive charge : 355.4073 centred at (gu) : 91.92020 90.98845 91.02865 assigned negative charge : -352.0016 centred at (gu) : 92.13561 91.45248 91.44276 start vw surface at 0.1100000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 83802 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20415 grid for indexing accessible points = 1.400000 m= 33152 mr = 58352 m= 6400 mr = 24876 m= 594 mr = 4117 m= 17 mr = 298 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 1420 time to turn everything in is 0.7200000 number of dielectric boundary points 36322 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 17420 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) : 0.7059290 object centre at (A) : 5.936000 4.500999 26.04300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8159148E-02 6.4144037E-03 midg,1,midg; midg,igrid,midg -1.6275965E-02 -0.1057426 1,midg,midg; igrid,midg,midg -3.8660469E-03 9.9296942E-03 gauss-seidel spectral radius is 0.9988589 estimated iterations to convergence 234 setup time was (sec) 1.100000 now iterating at: 13:38:00 rms-change max change #iterations 4.974188 218.4565 at 10iterations 2.475419 75.57700 at 20iterations 1.230935 36.47448 at 30iterations 0.6154795 17.54623 at 40iterations 0.3082701 8.726639 at 50iterations 0.1542928 4.931690 at 60iterations 7.7067174E-02 2.511108 at 70iterations 3.8787562E-02 1.090492 at 80iterations 1.9636972E-02 0.5600891 at 90iterations 1.0007120E-02 0.2784119 at 100iterations 5.2271411E-03 0.1734543 at 110iterations 2.8462745E-03 8.8762283E-02 at 120iterations finished qdiffx linear iterations at : 13:38:11 total time elapsed so far: 12.16000 # loops : 120 mean,max change (kT/e) : 2.8462745E-03 8.8762283E-02 energy calculations done at 12.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.33000 DelPhi exited at 13:38:11 12.332u 0.496s 0:13.09 97.9% 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 13:38:11 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2339 !!! WARNING: GLM 182 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.176681 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): -18.51800 30.39000 ymin,ymax (A): -20.71400 29.71600 zmin,zma (A): 4.075000 48.01100 x,y,z range (A): 48.90800 50.43000 43.93600 scale (grids/A): 3.176681 object centre (A): 5.936000 4.500999 26.04300 number of atom coordinates read : 2339 total number of charged atoms : 2195 net assigned charge : 3.406011 assigned positive charge : 355.4073 centred at (gu) : 92.88016 91.48250 91.54292 assigned negative charge : -352.0016 centred at (gu) : 93.20341 92.17857 92.16405 start vw surface at 0.1100000 fill in re-entrant regions at 0.8600000 boundary points on vw surface= 192931 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20415 grid for indexing accessible points = 1.400000 m= 103072 mr = 140520 m= 41989 mr = 84997 m= 11934 mr = 34236 m= 2406 mr = 9086 m= 251 mr = 1713 m= 11 mr = 118 m= 0 mr = 6 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 4959 time to turn everything in is 2.200000 number of dielectric boundary points 81918 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.390000 number of grid points assigned charge 17560 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) : 2.117787 object centre at (A) : 5.936000 4.500999 26.04300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6221744 3.0197473E-02 midg,1,midg; midg,igrid,midg -0.5711608 -1.181972 1,midg,midg; igrid,midg,midg -0.1169578 1.5853008E-02 gauss-seidel spectral radius is 0.9993081 estimated iterations to convergence 300 setup time was (sec) 2.610000 now iterating at: 13:38:14 rms-change max change #iterations 11.09106 455.6353 at 10iterations 6.645499 156.7998 at 20iterations 3.964593 77.27075 at 30iterations 2.356292 42.94125 at 40iterations 1.398315 25.86228 at 50iterations 0.8274942 15.49049 at 60iterations 0.4881178 8.230568 at 70iterations 0.2884040 5.307023 at 80iterations 0.1699214 2.888255 at 90iterations 0.1004375 1.887905 at 100iterations 5.9305362E-02 0.9416656 at 110iterations 3.5111271E-02 0.6095085 at 120iterations 2.0986810E-02 0.3964996 at 130iterations 1.2756140E-02 0.2158813 at 140iterations 7.9967212E-03 0.1580582 at 150iterations 5.2521261E-03 0.1039047 at 160iterations 3.6805752E-03 7.4588776E-02 at 170iterations 2.7591570E-03 6.0174942E-02 at 180iterations finished qdiffx linear iterations at : 13:38:33 total time elapsed so far: 21.30000 # loops : 180 mean,max change (kT/e) : 2.7591570E-03 6.0174942E-02 energy calculations done at 21.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.47000 DelPhi exited at 13:38:34 21.473u 0.531s 0:22.27 98.7% 0+0k 0+0io 0pf+0w