Fri Feb 3 15:27:26 PST 2012 #!/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 Fri Feb 3 2012 at 15:27:26 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 ! Automatically converted by prot2crg.py # of charge parameter records: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3809 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5360477 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): -27.48200 38.93000 ymin,ymax (A): 1.444000 55.11700 zmin,zma (A): -33.48600 25.52900 x,y,z range (A): 66.41200 53.67300 59.01500 scale (grids/A): 0.5360477 object centre (A): 5.724000 28.28050 -3.978500 number of atom coordinates read : 3809 total number of charged atoms : 3661 net assigned charge : 1.8358231E-05 assigned positive charge : 566.5783 centred at (gu) : 89.84369 89.33633 91.45123 assigned negative charge : -566.5803 centred at (gu) : 89.79984 89.35248 91.54531 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7013 nv = 96 ne = 84 npr = 78642 no. pairs analyzed = 78642 no. exposed pairs = 4768 no. arc points = 33603 no. surface atoms = 1603 nbur = 2206 mkacc time = 0.1300000 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 = 1.568000 m= 286 mr = 3637 m= 0 mr = 8 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3654 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3312 ## 373 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 9290 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7824696E-10 -7.8865237E-10 midg,1,midg; midg,igrid,midg 1.2106771E-10 -7.1479107E-11 1,midg,midg; igrid,midg,midg -2.5625999E-10 2.5090760E-10 gauss-seidel spectral radius is 0.9821298 estimated iterations to convergence 62 setup time was (sec) 0.4600000 now iterating at: 15:27:27 rms-change max change #iterations 7.6422751E-02 10.58078 at 10iterations 4.9252044E-03 0.7724581 at 20iterations 3.5493271E-04 6.7382813E-02 at 30iterations 4.6716417E-05 1.2010574E-02 at 40iterations 1.0187724E-05 2.7732849E-03 at 50iterations finished qdiffx linear iterations at : 15:27:29 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 1.0187724E-05 2.7732849E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 15:27:30 3.491u 0.178s 0:03.67 99.7% 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 Fri Feb 3 2012 at 15:27:30 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 ! Automatically converted by prot2crg.py # of charge parameter records: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3809 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.608143 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): -27.48200 38.93000 ymin,ymax (A): 1.444000 55.11700 zmin,zma (A): -33.48600 25.52900 x,y,z range (A): 66.41200 53.67300 59.01500 scale (grids/A): 1.608143 object centre (A): 5.724000 28.28050 -3.978500 number of atom coordinates read : 3809 total number of charged atoms : 3661 net assigned charge : 1.8358231E-05 assigned positive charge : 566.5783 centred at (gu) : 89.53004 88.00789 94.35278 assigned negative charge : -566.5803 centred at (gu) : 89.39914 88.05678 94.63512 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 78491 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33603 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 24064 mr = 53567 m= 2493 mr = 16498 m= 42 mr = 1234 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 125 time to turn everything in is 0.4100000 number of dielectric boundary points 33791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 341 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 27943 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) : 0.5360477 object centre at (A) : 5.724000 28.28050 -3.978500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2659077E-03 -1.5753441E-02 midg,1,midg; midg,igrid,midg 1.0705630E-02 4.4587436E-03 1,midg,midg; igrid,midg,midg 5.1732926E-04 -7.6188552E-03 gauss-seidel spectral radius is 0.9982213 estimated iterations to convergence 188 setup time was (sec) 0.6400000 now iterating at: 15:27:31 rms-change max change #iterations 3.715969 220.5677 at 10iterations 1.560902 53.84579 at 20iterations 0.6552103 22.00684 at 30iterations 0.2764514 8.997190 at 40iterations 0.1160486 4.107247 at 50iterations 4.8921704E-02 1.746162 at 60iterations 2.0658527E-02 0.7146566 at 70iterations 8.6766900E-03 0.2938814 at 80iterations 3.6666368E-03 0.1435480 at 90iterations 1.5457433E-03 5.0584793E-02 at 100iterations 6.5335399E-04 2.1626472E-02 at 110iterations 2.7632405E-04 9.4604492E-03 at 120iterations finished qdiffx linear iterations at : 15:27:38 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 2.7632405E-04 9.4604492E-03 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 15:27:38 7.926u 0.216s 0:08.39 96.9% 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 Fri Feb 3 2012 at 15:27:38 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 ! Automatically converted by prot2crg.py # of charge parameter records: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3809 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.412215 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): -27.48200 38.93000 ymin,ymax (A): 1.444000 55.11700 zmin,zma (A): -33.48600 25.52900 x,y,z range (A): 66.41200 53.67300 59.01500 scale (grids/A): 2.412215 object centre (A): 5.724000 28.28050 -3.978500 number of atom coordinates read : 3809 total number of charged atoms : 3661 net assigned charge : 1.8358231E-05 assigned positive charge : 566.5783 centred at (gu) : 89.29481 87.01134 96.52877 assigned negative charge : -566.5803 centred at (gu) : 89.09878 87.08507 96.95235 start vw surface at 0.1100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 182975 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33603 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 83300 mr = 131573 m= 23750 mr = 65645 m= 3847 mr = 17911 m= 219 mr = 2517 m= 1 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 504 time to turn everything in is 0.9500000 number of dielectric boundary points 76341 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 29247 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) : 1.608143 object centre at (A) : 5.724000 28.28050 -3.978500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1442256 -0.2258487 midg,1,midg; midg,igrid,midg 0.1751791 9.0869300E-02 1,midg,midg; igrid,midg,midg 0.1513990 -6.4005367E-02 gauss-seidel spectral radius is 0.9991721 estimated iterations to convergence 274 setup time was (sec) 1.210000 now iterating at: 15:27:40 rms-change max change #iterations 9.615528 381.9215 at 10iterations 5.455192 138.8210 at 20iterations 3.069258 63.94013 at 30iterations 1.723715 34.21422 at 40iterations 0.9661305 23.12486 at 50iterations 0.5411796 10.14503 at 60iterations 0.3022259 5.619310 at 70iterations 0.1690565 3.445250 at 80iterations 9.3985930E-02 1.693569 at 90iterations 5.2317377E-02 1.135948 at 100iterations 2.9143268E-02 0.5355968 at 110iterations 1.6218472E-02 0.3174782 at 120iterations 9.0326611E-03 0.1756611 at 130iterations 5.0174906E-03 9.4251633E-02 at 140iterations 2.7912518E-03 5.3813934E-02 at 150iterations 1.5544771E-03 3.0114293E-02 at 160iterations 8.6447207E-04 1.6695119E-02 at 170iterations 4.8081155E-04 9.0909004E-03 at 180iterations finished qdiffx linear iterations at : 15:27:52 total time elapsed so far: 12.67000 # loops : 180 mean,max change (kT/e) : 4.8081155E-04 9.0909004E-03 energy calculations done at 12.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 15:27:52 12.809u 0.222s 0:13.77 94.5% 0+0k 0+0io 0pf+0w