Mon Oct 10 09:12:42 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 Mon Oct 10 2011 at 09:12:42 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6534388 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): -5.581000 34.25500 ymin,ymax (A): -3.352000 49.14400 zmin,zma (A): -23.66200 30.81900 x,y,z range (A): 39.83600 52.49600 54.48100 scale (grids/A): 0.6534388 object centre (A): 14.33700 22.89600 3.578501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 292.2259 centred at (gu) : 90.68098 92.33118 90.06758 assigned negative charge : -289.2262 centred at (gu) : 90.77904 92.44522 90.00854 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5697 nv = 96 ne = 84 npr = 40527 no. pairs analyzed = 40527 no. exposed pairs = 2503 no. arc points = 17632 no. surface atoms = 849 nbur = 1115 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 293 mr = 3161 m= 0 mr = 26 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.1700000 number of dielectric boundary points 2803 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1800 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6760 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1726667E-10 1.4256246E-08 midg,1,midg; midg,igrid,midg 1.2775563E-08 -1.2672929E-08 1,midg,midg; igrid,midg,midg 1.6298818E-08 -6.3491470E-09 gauss-seidel spectral radius is 0.9878066 estimated iterations to convergence 74 setup time was (sec) 0.3600000 now iterating at: 09:12:43 rms-change max change #iterations 0.1392348 21.19935 at 10iterations 1.4536356E-02 2.277626 at 20iterations 1.4903040E-03 0.2450256 at 30iterations 1.5391684E-04 2.1011353E-02 at 40iterations 1.6051032E-05 2.2563934E-03 at 50iterations finished qdiffx linear iterations at : 09:12:45 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.6051032E-05 2.2563934E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 09:12:46 3.373u 0.161s 0:03.80 92.8% 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 Mon Oct 10 2011 at 09:12:46 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.960316 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): -5.581000 34.25500 ymin,ymax (A): -3.352000 49.14400 zmin,zma (A): -23.66200 30.81900 x,y,z range (A): 39.83600 52.49600 54.48100 scale (grids/A): 1.960316 object centre (A): 14.33700 22.89600 3.578501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 292.2259 centred at (gu) : 92.04280 96.99344 90.20273 assigned negative charge : -289.2262 centred at (gu) : 92.33741 97.33598 90.02568 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 60984 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17632 grid for indexing accessible points = 1.400000 m= 22019 mr = 41628 m= 3355 mr = 16628 m= 158 mr = 2190 m= 0 mr = 54 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1955 time to turn everything in is 0.3000000 number of dielectric boundary points 26016 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 14453 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) : 0.6534388 object centre at (A) : 14.33700 22.89600 3.578501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8310939E-02 1.2640599E-02 midg,1,midg; midg,igrid,midg 3.5346661E-02 -1.3920073E-02 1,midg,midg; igrid,midg,midg 7.8278482E-03 -4.5338352E-03 gauss-seidel spectral radius is 0.9986337 estimated iterations to convergence 214 setup time was (sec) 0.5200000 now iterating at: 09:12:47 rms-change max change #iterations 3.842946 168.1094 at 10iterations 1.803603 63.78677 at 20iterations 0.8442010 30.81381 at 30iterations 0.3950827 13.06288 at 40iterations 0.1841842 6.523905 at 50iterations 8.6321786E-02 3.077987 at 60iterations 4.0311303E-02 1.468006 at 70iterations 1.8840298E-02 0.6034393 at 80iterations 8.7866047E-03 0.2881699 at 90iterations 4.1152379E-03 0.1458654 at 100iterations 1.9321616E-03 7.2253346E-02 at 110iterations 9.0247596E-04 3.0873775E-02 at 120iterations finished qdiffx linear iterations at : 09:12:54 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 9.0247596E-04 3.0873775E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 09:12:54 7.707u 0.206s 0:08.16 96.8% 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 Mon Oct 10 2011 at 09:12:54 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.940475 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): -5.581000 34.25500 ymin,ymax (A): -3.352000 49.14400 zmin,zma (A): -23.66200 30.81900 x,y,z range (A): 39.83600 52.49600 54.48100 scale (grids/A): 2.940475 object centre (A): 14.33700 22.89600 3.578501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 292.2259 centred at (gu) : 93.06429 100.4902 90.30413 assigned negative charge : -289.2262 centred at (gu) : 93.50609 101.0040 90.03838 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 140911 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17632 grid for indexing accessible points = 1.400000 m= 70933 mr = 100762 m= 25819 mr = 58504 m= 5940 mr = 21357 m= 746 mr = 4548 m= 40 mr = 506 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 6772 time to turn everything in is 0.8100000 number of dielectric boundary points 58696 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 14655 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) : 1.960316 object centre at (A) : 14.33700 22.89600 3.578501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9743501 -1.8167745E-03 midg,1,midg; midg,igrid,midg 0.3400245 -0.1728415 1,midg,midg; igrid,midg,midg 5.0057609E-02 -2.4724502E-02 gauss-seidel spectral radius is 0.9992477 estimated iterations to convergence 288 setup time was (sec) 1.030000 now iterating at: 09:12:55 rms-change max change #iterations 8.936119 468.8117 at 10iterations 5.125514 123.7309 at 20iterations 2.929792 62.73079 at 30iterations 1.673230 32.68580 at 40iterations 0.9573660 20.71962 at 50iterations 0.5462322 11.29289 at 60iterations 0.3107072 6.767958 at 70iterations 0.1775168 3.426041 at 80iterations 0.1011261 2.129253 at 90iterations 5.7627782E-02 1.150894 at 100iterations 3.2849822E-02 0.6047859 at 110iterations 1.8806301E-02 0.4027338 at 120iterations 1.0709792E-02 0.2050491 at 130iterations 6.1166114E-03 0.1145554 at 140iterations 3.4913435E-03 7.2219849E-02 at 150iterations 1.9906287E-03 3.6567688E-02 at 160iterations 1.1334225E-03 2.5733948E-02 at 170iterations 6.4630673E-04 1.1874199E-02 at 180iterations finished qdiffx linear iterations at : 09:13:06 total time elapsed so far: 12.17000 # loops : 180 mean,max change (kT/e) : 6.4630673E-04 1.1874199E-02 energy calculations done at 12.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.30000 DelPhi exited at 09:13:07 12.301u 0.201s 0:12.90 96.8% 0+0k 0+0io 0pf+0w