Tue Oct 11 06:57:56 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 06:57:56 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 = 2950 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5346389 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): -19.73800 46.84900 ymin,ymax (A): 21.48200 79.21200 zmin,zma (A): -72.41000 -23.36600 x,y,z range (A): 66.58700 57.73000 49.04400 scale (grids/A): 0.5346389 object centre (A): 13.55550 50.34700 -47.88800 number of atom coordinates read : 2950 total number of charged atoms : 2810 net assigned charge : -1.499992 assigned positive charge : 431.2555 centred at (gu) : 88.93594 89.60082 90.10019 assigned negative charge : -432.7562 centred at (gu) : 88.92856 89.69187 90.13096 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5464 nv = 96 ne = 84 npr = 59917 no. pairs analyzed = 59917 no. exposed pairs = 3795 no. arc points = 26991 no. surface atoms = 1275 nbur = 1675 mkacc time = 0.1400000 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 = 1.596000 m= 250 mr = 2791 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 2914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2703 ## 354 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7236 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6357995E-11 -1.9468635E-10 midg,1,midg; midg,igrid,midg 3.5150002E-10 -4.0332906E-10 1,midg,midg; igrid,midg,midg -1.1918945E-10 -2.2988720E-11 gauss-seidel spectral radius is 0.9819744 estimated iterations to convergence 61 setup time was (sec) 0.5800000 now iterating at: 06:57:57 rms-change max change #iterations 6.4146005E-02 11.07504 at 10iterations 4.1159503E-03 0.7224998 at 20iterations 2.7106015E-04 5.3192139E-02 at 30iterations 2.4302512E-05 5.4368973E-03 at 40iterations 3.4033330E-06 8.7928772E-04 at 50iterations finished qdiffx linear iterations at : 06:58:00 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 3.4033330E-06 8.7928772E-04 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 06:58:00 3.466u 0.158s 0:04.08 88.4% 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 Tue Oct 11 2011 at 06:58:00 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 = 2950 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.603917 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): -19.73800 46.84900 ymin,ymax (A): 21.48200 79.21200 zmin,zma (A): -72.41000 -23.36600 x,y,z range (A): 66.58700 57.73000 49.04400 scale (grids/A): 1.603917 object centre (A): 13.55550 50.34700 -47.88800 number of atom coordinates read : 2950 total number of charged atoms : 2810 net assigned charge : -1.499992 assigned positive charge : 431.2555 centred at (gu) : 86.80736 88.80170 90.29973 assigned negative charge : -432.7562 centred at (gu) : 86.78522 89.07520 90.39251 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 60601 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26991 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 19243 mr = 40226 m= 2120 mr = 13536 m= 43 mr = 1119 m= 0 mr = 1 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 27125 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 283 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 21410 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) : 0.5346389 object centre at (A) : 13.55550 50.34700 -47.88800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6520311E-03 6.6874246E-03 midg,1,midg; midg,igrid,midg -2.0402379E-03 5.0994693E-03 1,midg,midg; igrid,midg,midg -1.4019141E-04 -2.2731874E-02 gauss-seidel spectral radius is 0.9981228 estimated iterations to convergence 183 setup time was (sec) 0.7800000 now iterating at: 06:58:01 rms-change max change #iterations 3.129097 155.2450 at 10iterations 1.282115 58.63339 at 20iterations 0.5252538 27.54976 at 30iterations 0.2159936 8.347075 at 40iterations 8.9031287E-02 3.415253 at 50iterations 3.6461182E-02 1.353670 at 60iterations 1.4998316E-02 0.5686817 at 70iterations 6.1929557E-03 0.2429256 at 80iterations 2.5409132E-03 9.4392300E-02 at 90iterations 1.0493133E-03 3.8387299E-02 at 100iterations 4.3355318E-04 1.5550613E-02 at 110iterations 1.8026379E-04 7.3127747E-03 at 120iterations finished qdiffx linear iterations at : 06:58:08 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 1.8026379E-04 7.3127747E-03 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 06:58:09 7.583u 0.201s 0:08.40 92.6% 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 06:58:09 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 = 2950 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: 2.405875 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): -19.73800 46.84900 ymin,ymax (A): 21.48200 79.21200 zmin,zma (A): -72.41000 -23.36600 x,y,z range (A): 66.58700 57.73000 49.04400 scale (grids/A): 2.405875 object centre (A): 13.55550 50.34700 -47.88800 number of atom coordinates read : 2950 total number of charged atoms : 2810 net assigned charge : -1.499992 assigned positive charge : 431.2555 centred at (gu) : 85.21095 88.20226 90.44966 assigned negative charge : -432.7562 centred at (gu) : 85.17765 88.61263 90.58871 start vw surface at 0.2400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 140659 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26991 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 65743 mr = 98706 m= 19803 mr = 52169 m= 3256 mr = 15361 m= 183 mr = 2259 m= 2 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.200000 number of dielectric boundary points 61081 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 22454 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) : 1.603917 object centre at (A) : 13.55550 50.34700 -47.88800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8248801E-02 0.1257271 midg,1,midg; midg,igrid,midg -6.1928473E-02 0.1150028 1,midg,midg; igrid,midg,midg -4.6460360E-02 -0.6773720 gauss-seidel spectral radius is 0.9991241 estimated iterations to convergence 267 setup time was (sec) 1.520000 now iterating at: 06:58:11 rms-change max change #iterations 8.168225 300.8824 at 10iterations 4.545961 123.0939 at 20iterations 2.521343 56.96217 at 30iterations 1.391705 31.49414 at 40iterations 0.7675403 17.67336 at 50iterations 0.4225518 11.96572 at 60iterations 0.2317297 5.392015 at 70iterations 0.1270897 2.827423 at 80iterations 6.9573089E-02 1.518675 at 90iterations 3.8153384E-02 0.8414256 at 100iterations 2.0905873E-02 0.5105610 at 110iterations 1.1420616E-02 0.2392030 at 120iterations 6.2439218E-03 0.1364784 at 130iterations 3.4170158E-03 7.1530819E-02 at 140iterations 1.8625709E-03 4.2977333E-02 at 150iterations 1.0187554E-03 2.2795677E-02 at 160iterations 5.5646728E-04 1.2597084E-02 at 170iterations 3.0405764E-04 6.3734055E-03 at 180iterations finished qdiffx linear iterations at : 06:58:22 total time elapsed so far: 12.56000 # loops : 180 mean,max change (kT/e) : 3.0405764E-04 6.3734055E-03 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.78000 DelPhi exited at 06:58:23 12.779u 0.185s 0:14.74 87.8% 0+0k 0+0io 0pf+0w