Sat Oct 15 13:37:44 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 Sat Oct 15 2011 at 13:37:44 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 = 2817 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: 0.6306689 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): -46.76500 7.938000 ymin,ymax (A): -28.99300 27.45500 zmin,zma (A): -7.866000 41.28800 x,y,z range (A): 54.70300 56.44800 49.15400 scale (grids/A): 0.6306689 object centre (A): -19.41350 -0.7690001 16.71100 number of atom coordinates read : 2817 total number of charged atoms : 2669 net assigned charge : -0.4999833 assigned positive charge : 429.9503 centred at (gu) : 90.29443 90.42963 89.56448 assigned negative charge : -430.4511 centred at (gu) : 90.46569 90.41255 89.85503 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7350 nv = 96 ne = 84 npr = 57506 no. pairs analyzed = 57506 no. exposed pairs = 3373 no. arc points = 23486 no. surface atoms = 1135 nbur = 1682 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 352 mr = 4127 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 92 time to turn everything in is 0.2100000 number of dielectric boundary points 3550 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2338 ## 220 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9035 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0347298E-08 -2.7787868E-08 midg,1,midg; midg,igrid,midg -2.0906237E-09 1.2338695E-09 1,midg,midg; igrid,midg,midg 1.5197593E-08 -1.9254140E-08 gauss-seidel spectral radius is 0.9869907 estimated iterations to convergence 72 setup time was (sec) 0.3900000 now iterating at: 13:37:45 rms-change max change #iterations 0.1423079 21.90210 at 10iterations 1.3737985E-02 2.329916 at 20iterations 1.3280605E-03 0.1757965 at 30iterations 1.5013448E-04 2.6964188E-02 at 40iterations 3.2753924E-05 6.3428879E-03 at 50iterations finished qdiffx linear iterations at : 13:37:49 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 3.2753924E-05 6.3428879E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 13:37:50 3.456u 0.218s 0:05.41 67.6% 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 Sat Oct 15 2011 at 13:37:50 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 = 2817 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: 1.892007 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): -46.76500 7.938000 ymin,ymax (A): -28.99300 27.45500 zmin,zma (A): -7.866000 41.28800 x,y,z range (A): 54.70300 56.44800 49.15400 scale (grids/A): 1.892007 object centre (A): -19.41350 -0.7690001 16.71100 number of atom coordinates read : 2817 total number of charged atoms : 2669 net assigned charge : -0.4999833 assigned positive charge : 429.9503 centred at (gu) : 90.88227 91.28835 88.69278 assigned negative charge : -430.4511 centred at (gu) : 91.39671 91.23740 89.56475 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 80308 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23486 grid for indexing accessible points = 1.400000 m= 27504 mr = 56840 m= 3769 mr = 20092 m= 183 mr = 2168 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 3029 time to turn everything in is 0.3800000 number of dielectric boundary points 32621 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 20994 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) : 0.6306689 object centre at (A) : -19.41350 -0.7690001 16.71100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5297888E-02 -8.4500216E-02 midg,1,midg; midg,igrid,midg -5.5009429E-03 -2.6192633E-03 1,midg,midg; igrid,midg,midg 5.6165047E-02 -1.6705038E-02 gauss-seidel spectral radius is 0.9986313 estimated iterations to convergence 214 setup time was (sec) 0.5900000 now iterating at: 13:37:51 rms-change max change #iterations 4.413648 170.7395 at 10iterations 2.073507 67.68134 at 20iterations 0.9726403 29.86237 at 30iterations 0.4571967 15.06550 at 40iterations 0.2138110 6.562300 at 50iterations 0.1007831 2.936334 at 60iterations 4.7168821E-02 1.430589 at 70iterations 2.2188392E-02 0.6833076 at 80iterations 1.0414881E-02 0.3146591 at 90iterations 4.8804805E-03 0.1408796 at 100iterations 2.2984107E-03 8.3965302E-02 at 110iterations 1.0817824E-03 3.2817841E-02 at 120iterations finished qdiffx linear iterations at : 13:38:03 total time elapsed so far: 8.170000 # loops : 120 mean,max change (kT/e) : 1.0817824E-03 3.2817841E-02 energy calculations done at 8.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.300000 DelPhi exited at 13:38:04 8.302u 0.246s 0:14.07 60.6% 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 Sat Oct 15 2011 at 13:38:04 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 = 2817 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: 2.838010 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): -46.76500 7.938000 ymin,ymax (A): -28.99300 27.45500 zmin,zma (A): -7.866000 41.28800 x,y,z range (A): 54.70300 56.44800 49.15400 scale (grids/A): 2.838010 object centre (A): -19.41350 -0.7690001 16.71100 number of atom coordinates read : 2817 total number of charged atoms : 2669 net assigned charge : -0.4999833 assigned positive charge : 429.9503 centred at (gu) : 91.32342 91.93240 88.03891 assigned negative charge : -430.4511 centred at (gu) : 92.09496 91.85599 89.34692 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 185951 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23486 grid for indexing accessible points = 1.400000 m= 91537 mr = 137832 m= 30581 mr = 74780 m= 6595 mr = 24136 m= 749 mr = 4703 m= 23 mr = 419 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 10235 time to turn everything in is 1.070000 number of dielectric boundary points 73566 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 21352 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) : 1.892007 object centre at (A) : -19.41350 -0.7690001 16.71100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2209553 -1.131012 midg,1,midg; midg,igrid,midg -0.1696642 -0.1515804 1,midg,midg; igrid,midg,midg 0.4627746 -0.4277598 gauss-seidel spectral radius is 0.9992607 estimated iterations to convergence 290 setup time was (sec) 1.340000 now iterating at: 13:38:06 rms-change max change #iterations 10.41133 300.3345 at 10iterations 6.142065 154.0668 at 20iterations 3.599297 77.25414 at 30iterations 2.098161 39.96906 at 40iterations 1.220306 25.65836 at 50iterations 0.7092471 14.59042 at 60iterations 0.4112246 7.610204 at 70iterations 0.2378539 4.024338 at 80iterations 0.1373996 2.607388 at 90iterations 7.9194665E-02 1.474742 at 100iterations 4.5791462E-02 0.8869405 at 110iterations 2.6387198E-02 0.4929695 at 120iterations 1.5217383E-02 0.2546177 at 130iterations 8.7837363E-03 0.1702118 at 140iterations 5.0689485E-03 8.5618973E-02 at 150iterations 2.9274276E-03 5.3642273E-02 at 160iterations 1.6979841E-03 3.3897400E-02 at 170iterations 9.9177239E-04 1.7534256E-02 at 180iterations finished qdiffx linear iterations at : 13:38:27 total time elapsed so far: 13.91000 # loops : 180 mean,max change (kT/e) : 9.9177239E-04 1.7534256E-02 energy calculations done at 13.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.05000 DelPhi exited at 13:38:28 14.054u 0.285s 0:23.53 60.9% 0+0k 0+0io 0pf+0w