Sat Oct 8 17:43:20 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+sph2.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 = amb2.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 8 2011 at 17:43:20 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3516 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5250815 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): -0.8780000 44.42900 ymin,ymax (A): -30.26400 26.20500 zmin,zma (A): 1.281000 69.08000 x,y,z range (A): 45.30700 56.46900 67.79900 scale (grids/A): 0.5250815 object centre (A): 21.77550 -2.029500 35.18050 number of atom coordinates read : 3516 total number of charged atoms : 3369 net assigned charge : -5.871982 assigned positive charge : 539.6921 centred at (gu) : 90.49901 91.73297 90.52499 assigned negative charge : -545.5659 centred at (gu) : 90.45841 91.69022 90.52232 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6102 nv = 96 ne = 84 npr = 72243 no. pairs analyzed = 72243 no. exposed pairs = 4271 no. arc points = 29053 no. surface atoms = 1449 nbur = 2067 mkacc time = 0.1500000 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 = 1.624000 m= 223 mr = 3238 m= 0 mr = 12 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3075 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3015 ## 459 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8220 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4838859E-10 -1.7086613E-10 midg,1,midg; midg,igrid,midg -2.0303660E-10 -4.8369616E-12 1,midg,midg; igrid,midg,midg -2.7009253E-10 -1.4857070E-11 gauss-seidel spectral radius is 0.9813490 estimated iterations to convergence 60 setup time was (sec) 0.6000000 now iterating at: 17:43:21 rms-change max change #iterations 6.6982351E-02 10.78377 at 10iterations 4.2577856E-03 0.6795197 at 20iterations 4.4303920E-04 8.2160950E-02 at 30iterations 1.0309666E-04 1.9418716E-02 at 40iterations 2.8027818E-05 5.0392151E-03 at 50iterations finished qdiffx linear iterations at : 17:43:24 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 2.8027818E-05 5.0392151E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 17:43:24 3.468u 0.237s 0:03.97 92.9% 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 Sat Oct 8 2011 at 17:43:24 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3516 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 1.575244 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): -0.8780000 44.42900 ymin,ymax (A): -30.26400 26.20500 zmin,zma (A): 1.281000 69.08000 x,y,z range (A): 45.30700 56.46900 67.79900 scale (grids/A): 1.575244 object centre (A): 21.77550 -2.029500 35.18050 number of atom coordinates read : 3516 total number of charged atoms : 3369 net assigned charge : -5.871982 assigned positive charge : 539.6921 centred at (gu) : 91.49617 95.19768 91.57401 assigned negative charge : -545.5659 centred at (gu) : 91.37472 95.07022 91.56665 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 69135 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29053 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20472 mr = 48118 m= 1837 mr = 13966 m= 42 mr = 798 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 28604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 442 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 25514 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) : 0.5250815 object centre at (A) : 21.77550 -2.029500 35.18050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8614522E-03 1.0823156E-02 midg,1,midg; midg,igrid,midg -8.3829993E-03 -1.1148115E-02 1,midg,midg; igrid,midg,midg -4.7014635E-03 1.4917174E-03 gauss-seidel spectral radius is 0.9980840 estimated iterations to convergence 182 setup time was (sec) 0.8000000 now iterating at: 17:43:25 rms-change max change #iterations 3.423197 162.3255 at 10iterations 1.393710 64.73132 at 20iterations 0.5668259 19.72043 at 30iterations 0.2316140 7.689600 at 40iterations 9.4523504E-02 3.939392 at 50iterations 3.8654685E-02 1.390958 at 60iterations 1.5808983E-02 0.5527840 at 70iterations 6.4413794E-03 0.2231841 at 80iterations 2.6485170E-03 9.5162392E-02 at 90iterations 1.0984653E-03 4.3196678E-02 at 100iterations 4.7008457E-04 1.9021988E-02 at 110iterations 2.0989182E-04 7.4119568E-03 at 120iterations finished qdiffx linear iterations at : 17:43:32 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 2.0989182E-04 7.4119568E-03 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 17:43:32 7.742u 0.244s 0:08.26 96.6% 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 8 2011 at 17:43:32 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3516 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.362867 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): -0.8780000 44.42900 ymin,ymax (A): -30.26400 26.20500 zmin,zma (A): 1.281000 69.08000 x,y,z range (A): 45.30700 56.46900 67.79900 scale (grids/A): 2.362867 object centre (A): 21.77550 -2.029500 35.18050 number of atom coordinates read : 3516 total number of charged atoms : 3369 net assigned charge : -5.871982 assigned positive charge : 539.6921 centred at (gu) : 92.24400 97.79629 92.36058 assigned negative charge : -545.5659 centred at (gu) : 92.06210 97.60520 92.34994 start vw surface at 0.1600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 160478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29053 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 73592 mr = 117767 m= 19356 mr = 58087 m= 2630 mr = 14176 m= 142 mr = 1608 m= 3 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 64534 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 39 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 26897 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) : 1.575244 object centre at (A) : 21.77550 -2.029500 35.18050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2665200 6.1835673E-02 midg,1,midg; midg,igrid,midg -0.1177610 -0.1571497 1,midg,midg; igrid,midg,midg -7.9945169E-02 5.0898314E-02 gauss-seidel spectral radius is 0.9991115 estimated iterations to convergence 265 setup time was (sec) 1.510000 now iterating at: 17:43:34 rms-change max change #iterations 9.049400 259.5118 at 10iterations 5.006507 127.1050 at 20iterations 2.769774 77.18661 at 30iterations 1.519372 38.41308 at 40iterations 0.8340178 19.04508 at 50iterations 0.4562505 9.477520 at 60iterations 0.2485026 5.180906 at 70iterations 0.1355947 2.664006 at 80iterations 7.3964328E-02 1.476349 at 90iterations 4.0306576E-02 0.8338056 at 100iterations 2.2029271E-02 0.4365635 at 110iterations 1.2014979E-02 0.2277431 at 120iterations 6.5512261E-03 0.1302662 at 130iterations 3.5785169E-03 7.7022552E-02 at 140iterations 1.9590990E-03 3.9096832E-02 at 150iterations 1.0785109E-03 2.4889946E-02 at 160iterations 5.9987395E-04 1.3017654E-02 at 170iterations 3.3986327E-04 6.8511963E-03 at 180iterations finished qdiffx linear iterations at : 17:43:45 total time elapsed so far: 12.31000 # loops : 180 mean,max change (kT/e) : 3.3986327E-04 6.8511963E-03 energy calculations done at 12.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.48000 DelPhi exited at 17:43:45 12.483u 0.254s 0:13.02 97.7% 0+0k 0+0io 0pf+0w