Sun Oct 9 03:54:25 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 03:54:25 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4712 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4029884 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): -2.359000 79.08000 ymin,ymax (A): -12.12600 56.42000 zmin,zma (A): -15.59200 72.74800 x,y,z range (A): 81.43900 68.54601 88.34000 scale (grids/A): 0.4029884 object centre (A): 38.36050 22.14700 28.57800 number of atom coordinates read : 4712 total number of charged atoms : 4395 net assigned charge : 20.30001 assigned positive charge : 689.4091 centred at (gu) : 86.14010 91.85259 83.33193 assigned negative charge : -669.1140 centred at (gu) : 86.00107 91.90260 83.22239 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 4452 nv = 96 ne = 84 npr = 94005 no. pairs analyzed = 94005 no. exposed pairs = 6221 no. arc points = 44520 no. surface atoms = 2081 nbur = 2631 mkacc time = 0.2100000 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 = 2.072000 m= 110 mr = 1920 m= 0 mr = 1 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 2641 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3225 ## 839 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 6100 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4466403E-13 1.7037896E-13 midg,1,midg; midg,igrid,midg 5.6168124E-13 6.8894662E-13 1,midg,midg; igrid,midg,midg -8.4750897E-13 4.5587275E-13 gauss-seidel spectral radius is 0.9686872 estimated iterations to convergence 47 setup time was (sec) 0.7100000 now iterating at: 03:54:26 rms-change max change #iterations 1.9669434E-02 3.857430 at 10iterations 2.0918390E-03 0.5257683 at 20iterations 4.3706482E-04 0.1027336 at 30iterations 9.2931637E-05 2.0629883E-02 at 40iterations 1.9823074E-05 4.2381287E-03 at 50iterations finished qdiffx linear iterations at : 03:54:29 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.9823074E-05 4.2381287E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 03:54:29 3.472u 0.192s 0:03.94 92.8% 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 03:54:29 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4712 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.208965 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): -2.359000 79.08000 ymin,ymax (A): -12.12600 56.42000 zmin,zma (A): -15.59200 72.74800 x,y,z range (A): 81.43900 68.54601 88.34000 scale (grids/A): 1.208965 object centre (A): 38.36050 22.14700 28.57800 number of atom coordinates read : 4712 total number of charged atoms : 4395 net assigned charge : 20.30001 assigned positive charge : 689.4091 centred at (gu) : 78.41882 95.55633 69.99415 assigned negative charge : -669.1140 centred at (gu) : 78.00305 95.70785 69.66720 start vw surface at 0.2000000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 53276 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44520 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.932000 m= 10244 mr = 33355 m= 384 mr = 5387 m= 0 mr = 37 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 461 time to turn everything in is 0.4600000 number of dielectric boundary points 25125 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 901 ## 47 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 29328 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) : 0.4029884 object centre at (A) : 38.36050 22.14700 28.57800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.9398196E-03 1.3985098E-03 midg,1,midg; midg,igrid,midg 1.5718378E-03 1.5144504E-03 1,midg,midg; igrid,midg,midg -3.7873950E-04 9.5589925E-04 gauss-seidel spectral radius is 0.9966946 estimated iterations to convergence 139 setup time was (sec) 0.7400000 now iterating at: 03:54:30 rms-change max change #iterations 1.971643 103.0564 at 10iterations 0.6037811 29.42350 at 20iterations 0.1859082 9.098526 at 30iterations 5.8051709E-02 2.673120 at 40iterations 1.8595451E-02 0.8176117 at 50iterations 6.3372785E-03 0.2813282 at 60iterations 2.5661206E-03 0.1115265 at 70iterations 1.2486274E-03 4.9402237E-02 at 80iterations 6.8405236E-04 2.6069641E-02 at 90iterations 3.9325084E-04 1.3853073E-02 at 100iterations 2.2987531E-04 8.0509186E-03 at 110iterations 1.3495017E-04 4.7245026E-03 at 120iterations finished qdiffx linear iterations at : 03:54:37 total time elapsed so far: 7.160000 # loops : 120 mean,max change (kT/e) : 1.3495017E-04 4.7245026E-03 energy calculations done at 7.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.330000 DelPhi exited at 03:54:37 7.334u 0.213s 0:07.86 95.9% 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 03:54:37 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4712 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.813448 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): -2.359000 79.08000 ymin,ymax (A): -12.12600 56.42000 zmin,zma (A): -15.59200 72.74800 x,y,z range (A): 81.43900 68.54601 88.34000 scale (grids/A): 1.813448 object centre (A): 38.36050 22.14700 28.57800 number of atom coordinates read : 4712 total number of charged atoms : 4395 net assigned charge : 20.30001 assigned positive charge : 689.4091 centred at (gu) : 72.62780 98.33420 59.99091 assigned negative charge : -669.1140 centred at (gu) : 72.00462 98.56178 59.50077 start vw surface at 0.1900000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 125709 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44520 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.932000 m= 42079 mr = 84446 m= 5712 mr = 29237 m= 281 mr = 3111 m= 6 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 1537 time to turn everything in is 0.9500000 number of dielectric boundary points 56926 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 327 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 34360 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) : 1.208965 object centre at (A) : 38.36050 22.14700 28.57800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3705281 1.9898454E-02 midg,1,midg; midg,igrid,midg 3.7865117E-02 2.8196029E-02 1,midg,midg; igrid,midg,midg 1.1057832E-02 1.6540324E-02 gauss-seidel spectral radius is 0.9985723 estimated iterations to convergence 210 setup time was (sec) 1.240000 now iterating at: 03:54:39 rms-change max change #iterations 6.213904 218.0900 at 10iterations 2.964980 92.58716 at 20iterations 1.404009 40.31071 at 30iterations 0.6632528 18.95727 at 40iterations 0.3104779 8.717618 at 50iterations 0.1448885 3.967615 at 60iterations 6.7699127E-02 1.790792 at 70iterations 3.1625234E-02 0.8165855 at 80iterations 1.4947812E-02 0.4285040 at 90iterations 7.1747284E-03 0.2035313 at 100iterations 3.5404495E-03 9.1355324E-02 at 110iterations 1.8458554E-03 4.8954010E-02 at 120iterations 1.0418069E-03 2.7713776E-02 at 130iterations 6.3480745E-04 1.5491247E-02 at 140iterations 4.0957873E-04 9.4947815E-03 at 150iterations 2.7415546E-04 6.0672760E-03 at 160iterations 1.8763963E-04 4.0225983E-03 at 170iterations 1.2932945E-04 2.6760101E-03 at 180iterations finished qdiffx linear iterations at : 03:54:50 total time elapsed so far: 12.97000 # loops : 180 mean,max change (kT/e) : 1.2932945E-04 2.6760101E-03 energy calculations done at 12.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.15000 DelPhi exited at 03:54:51 13.153u 0.227s 0:13.66 97.8% 0+0k 0+0io 0pf+0w