Tue Oct 11 06:49:10 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 06:49:10 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 = 4070 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5035218 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): -8.484000 62.21800 ymin,ymax (A): 49.10600 109.4450 zmin,zma (A): 65.22300 112.9220 x,y,z range (A): 70.70200 60.33900 47.69901 scale (grids/A): 0.5035218 object centre (A): 26.86700 79.27550 89.07250 number of atom coordinates read : 4070 total number of charged atoms : 3924 net assigned charge : -1.999980 assigned positive charge : 612.2617 centred at (gu) : 89.37930 87.93157 89.42312 assigned negative charge : -614.2648 centred at (gu) : 89.51069 87.91666 89.50378 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6555 nv = 96 ne = 84 npr = 80745 no. pairs analyzed = 80745 no. exposed pairs = 5202 no. arc points = 36799 no. surface atoms = 1746 nbur = 2324 mkacc time = 0.2300000 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 = 1.708000 m= 242 mr = 3254 m= 0 mr = 6 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 3537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3510 ## 540 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 8771 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2662005E-10 -1.3284843E-10 midg,1,midg; midg,igrid,midg -8.1074210E-11 9.8060579E-13 1,midg,midg; igrid,midg,midg 2.2335712E-10 -2.0332418E-10 gauss-seidel spectral radius is 0.9797894 estimated iterations to convergence 58 setup time was (sec) 0.7300000 now iterating at: 06:49:11 rms-change max change #iterations 5.6212027E-02 9.285439 at 10iterations 3.2076458E-03 0.6350861 at 20iterations 2.7583924E-04 3.9558411E-02 at 30iterations 4.8124210E-05 5.8269501E-03 at 40iterations 1.0244507E-05 1.2207031E-03 at 50iterations finished qdiffx linear iterations at : 06:49:14 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 1.0244507E-05 1.2207031E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 06:49:14 4.211u 0.276s 0:04.83 92.7% 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 06:49:14 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 = 4070 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.510565 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): -8.484000 62.21800 ymin,ymax (A): 49.10600 109.4450 zmin,zma (A): 65.22300 112.9220 x,y,z range (A): 70.70200 60.33900 47.69901 scale (grids/A): 1.510565 object centre (A): 26.86700 79.27550 89.07250 number of atom coordinates read : 4070 total number of charged atoms : 3924 net assigned charge : -1.999980 assigned positive charge : 612.2617 centred at (gu) : 88.13656 83.79314 88.26823 assigned negative charge : -614.2648 centred at (gu) : 88.53170 83.74957 88.51094 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 74816 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36799 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 20440 mr = 49939 m= 1551 mr = 13218 m= 26 mr = 557 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 343 time to turn everything in is 0.6700000 number of dielectric boundary points 33119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 496 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 29385 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) : 0.5035218 object centre at (A) : 26.86700 79.27550 89.07250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2338601E-03 -2.5139640E-03 midg,1,midg; midg,igrid,midg -7.9118954E-03 -3.9299815E-03 1,midg,midg; igrid,midg,midg 4.4365931E-02 9.2257364E-03 gauss-seidel spectral radius is 0.9979774 estimated iterations to convergence 177 setup time was (sec) 0.9700000 now iterating at: 06:49:16 rms-change max change #iterations 3.350517 159.5339 at 10iterations 1.330897 55.37777 at 20iterations 0.5285638 17.88947 at 30iterations 0.2104286 8.338955 at 40iterations 8.3909906E-02 3.050468 at 50iterations 3.3477813E-02 1.208610 at 60iterations 1.3280692E-02 0.4743614 at 70iterations 5.3045484E-03 0.2253265 at 80iterations 2.1197051E-03 8.1085205E-02 at 90iterations 8.5059158E-04 2.9947281E-02 at 100iterations 3.4255977E-04 1.2906075E-02 at 110iterations 1.4008922E-04 4.6920776E-03 at 120iterations finished qdiffx linear iterations at : 06:49:24 total time elapsed so far: 9.210000 # loops : 120 mean,max change (kT/e) : 1.4008922E-04 4.6920776E-03 energy calculations done at 9.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.390000 DelPhi exited at 06:49:25 9.390u 0.297s 0:10.08 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 06:49:25 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4070 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.265848 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): -8.484000 62.21800 ymin,ymax (A): 49.10600 109.4450 zmin,zma (A): 65.22300 112.9220 x,y,z range (A): 70.70200 60.33900 47.69901 scale (grids/A): 2.265848 object centre (A): 26.86700 79.27550 89.07250 number of atom coordinates read : 4070 total number of charged atoms : 3924 net assigned charge : -1.999980 assigned positive charge : 612.2617 centred at (gu) : 87.20456 80.68944 87.40198 assigned negative charge : -614.2648 centred at (gu) : 87.79740 80.62434 87.76633 start vw surface at 0.1900000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 174628 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36799 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 74811 mr = 123055 m= 17322 mr = 57544 m= 1984 mr = 12174 m= 60 mr = 1121 m= 0 mr = 12 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 1153 time to turn everything in is 1.610000 number of dielectric boundary points 74899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 31291 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) : 1.510565 object centre at (A) : 26.86700 79.27550 89.07250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5649494E-02 -5.1901355E-02 midg,1,midg; midg,igrid,midg -0.1119287 -5.0867710E-02 1,midg,midg; igrid,midg,midg 0.9766673 0.2147464 gauss-seidel spectral radius is 0.9991017 estimated iterations to convergence 264 setup time was (sec) 1.930000 now iterating at: 06:49:27 rms-change max change #iterations 9.201122 318.5881 at 10iterations 5.184172 155.6492 at 20iterations 2.896146 93.62717 at 30iterations 1.609439 41.21277 at 40iterations 0.8887939 25.29748 at 50iterations 0.4891486 15.18883 at 60iterations 0.2687733 6.773178 at 70iterations 0.1475906 3.773990 at 80iterations 8.0706686E-02 1.977092 at 90iterations 4.4121597E-02 0.9983320 at 100iterations 2.4071356E-02 0.6114712 at 110iterations 1.3123251E-02 0.3080316 at 120iterations 7.1548452E-03 0.1639519 at 130iterations 3.8961612E-03 9.5238686E-02 at 140iterations 2.1224506E-03 4.0601254E-02 at 150iterations 1.1545346E-03 2.7142048E-02 at 160iterations 6.2776206E-04 1.4843941E-02 at 170iterations 3.4172644E-04 7.4057579E-03 at 180iterations finished qdiffx linear iterations at : 06:49:40 total time elapsed so far: 15.38000 # loops : 180 mean,max change (kT/e) : 3.4172644E-04 7.4057579E-03 energy calculations done at 15.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.55000 DelPhi exited at 06:49:41 15.552u 0.313s 0:16.26 97.5% 0+0k 0+0io 0pf+0w