Tue Oct 11 06:00:49 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 06:00:49 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 = 2081 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: 0.7046016 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): 16.27100 64.09700 ymin,ymax (A): -3.508000 33.47700 zmin,zma (A): 21.51900 72.04400 x,y,z range (A): 47.82600 36.98500 50.52500 scale (grids/A): 0.7046016 object centre (A): 40.18400 14.98450 46.78150 number of atom coordinates read : 2081 total number of charged atoms : 1953 net assigned charge : 6.500009 assigned positive charge : 316.0039 centred at (gu) : 90.88370 89.65847 88.69943 assigned negative charge : -309.5042 centred at (gu) : 91.00304 89.69432 88.63914 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7091 nv = 96 ne = 84 npr = 41484 no. pairs analyzed = 41484 no. exposed pairs = 2517 no. arc points = 17218 no. surface atoms = 857 nbur = 1224 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 475 mr = 4103 m= 3 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2600000 number of dielectric boundary points 3365 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1561 ## 150 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7804 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0478276E-08 6.2063194E-08 midg,1,midg; midg,igrid,midg 7.3119061E-08 3.3408305E-08 1,midg,midg; igrid,midg,midg 8.9510742E-08 -4.6747779E-09 gauss-seidel spectral radius is 0.9895024 estimated iterations to convergence 79 setup time was (sec) 0.5400000 now iterating at: 06:00:50 rms-change max change #iterations 0.1964412 25.10258 at 10iterations 2.4151677E-02 3.681694 at 20iterations 3.1483227E-03 0.4237175 at 30iterations 5.1854079E-04 6.5776825E-02 at 40iterations 1.2460037E-04 1.6759872E-02 at 50iterations finished qdiffx linear iterations at : 06:00:54 total time elapsed so far: 4.370000 # loops : 50 mean,max change (kT/e) : 1.2460037E-04 1.6759872E-02 energy calculations done at 4.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.550000 DelPhi exited at 06:00:55 4.554u 0.388s 0:05.58 88.3% 0+0k 0+0io 6pf+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 06:00:55 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 = 2081 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: 2.113805 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): 16.27100 64.09700 ymin,ymax (A): -3.508000 33.47700 zmin,zma (A): 21.51900 72.04400 x,y,z range (A): 47.82600 36.98500 50.52500 scale (grids/A): 2.113805 object centre (A): 40.18400 14.98450 46.78150 number of atom coordinates read : 2081 total number of charged atoms : 1953 net assigned charge : 6.500009 assigned positive charge : 316.0039 centred at (gu) : 92.65110 88.97530 86.09823 assigned negative charge : -309.5042 centred at (gu) : 93.00907 89.08311 85.91743 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 75593 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17218 grid for indexing accessible points = 1.400000 m= 31097 mr = 54127 m= 6232 mr = 23935 m= 552 mr = 4218 m= 11 mr = 294 m= 0 mr = 2 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 30909 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 15512 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) : 0.7046016 object centre at (A) : 40.18400 14.98450 46.78150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8223743E-02 4.6280935E-02 midg,1,midg; midg,igrid,midg 2.7503291E-02 1.2166656E-02 1,midg,midg; igrid,midg,midg 2.9930668E-02 2.7687706E-02 gauss-seidel spectral radius is 0.9988221 estimated iterations to convergence 231 setup time was (sec) 0.9200000 now iterating at: 06:00:56 rms-change max change #iterations 4.575922 176.9789 at 10iterations 2.268896 72.79292 at 20iterations 1.120889 37.10673 at 30iterations 0.5573321 16.80267 at 40iterations 0.2765682 8.347799 at 50iterations 0.1367740 4.083723 at 60iterations 6.8124324E-02 1.948066 at 70iterations 3.3723179E-02 0.9961967 at 80iterations 1.6862324E-02 0.4801102 at 90iterations 8.4426580E-03 0.3210068 at 100iterations 4.2593474E-03 0.1357155 at 110iterations 2.1951729E-03 6.4431906E-02 at 120iterations finished qdiffx linear iterations at : 06:01:06 total time elapsed so far: 10.55000 # loops : 120 mean,max change (kT/e) : 2.1951729E-03 6.4431906E-02 energy calculations done at 10.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.72000 DelPhi exited at 06:01:06 10.724u 0.444s 0:11.48 97.2% 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 06:01:06 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 = 2081 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: 3.170707 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): 16.27100 64.09700 ymin,ymax (A): -3.508000 33.47700 zmin,zma (A): 21.51900 72.04400 x,y,z range (A): 47.82600 36.98500 50.52500 scale (grids/A): 3.170707 object centre (A): 40.18400 14.98450 46.78150 number of atom coordinates read : 2081 total number of charged atoms : 1953 net assigned charge : 6.500009 assigned positive charge : 316.0039 centred at (gu) : 93.97657 88.46302 84.14729 assigned negative charge : -309.5042 centred at (gu) : 94.51362 88.62480 83.87631 start vw surface at 0.1100000 fill in re-entrant regions at 0.7600000 boundary points on vw surface= 174153 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17218 grid for indexing accessible points = 1.400000 m= 96600 mr = 130250 m= 40191 mr = 81085 m= 11846 mr = 33297 m= 2313 mr = 9323 m= 290 mr = 1675 m= 6 mr = 218 m= 0 mr = 2 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.950000 number of dielectric boundary points 69549 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 15624 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) : 2.113805 object centre at (A) : 40.18400 14.98450 46.78150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2845249 0.3033931 midg,1,midg; midg,igrid,midg 0.2098089 8.5291468E-02 1,midg,midg; igrid,midg,midg 0.2893996 0.4996932 gauss-seidel spectral radius is 0.9992923 estimated iterations to convergence 297 setup time was (sec) 2.270000 now iterating at: 06:01:09 rms-change max change #iterations 10.19679 351.4288 at 10iterations 6.026942 117.5700 at 20iterations 3.553610 84.99318 at 30iterations 2.097390 55.00212 at 40iterations 1.230557 23.90380 at 50iterations 0.7214248 17.44764 at 60iterations 0.4240575 8.182001 at 70iterations 0.2478012 4.558426 at 80iterations 0.1448859 2.510388 at 90iterations 8.4852576E-02 1.567790 at 100iterations 4.9595032E-02 0.8268433 at 110iterations 2.9158343E-02 0.5181627 at 120iterations 1.7130189E-02 0.3028488 at 130iterations 1.0154044E-02 0.1734066 at 140iterations 6.1197975E-03 0.1063118 at 150iterations 3.7646354E-03 6.2255859E-02 at 160iterations 2.4109122E-03 3.9104462E-02 at 170iterations 1.6274746E-03 2.6561737E-02 at 180iterations finished qdiffx linear iterations at : 06:01:25 total time elapsed so far: 18.23000 # loops : 180 mean,max change (kT/e) : 1.6274746E-03 2.6561737E-02 energy calculations done at 18.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.39000 DelPhi exited at 06:01:26 18.400u 0.461s 0:19.53 96.5% 0+0k 0+0io 0pf+0w