Sat Oct 8 19:13:05 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 19:13:05 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2595 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 0.6242548 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): -32.00200 18.27800 ymin,ymax (A): -24.32800 23.29400 zmin,zma (A): -12.46000 44.56800 x,y,z range (A): 50.28000 47.62200 57.02800 scale (grids/A): 0.6242548 object centre (A): -6.862000 -0.5170002 16.05400 number of atom coordinates read : 2595 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 88.33273 89.25214 89.90072 assigned negative charge : -390.0956 centred at (gu) : 88.22829 89.29562 89.79146 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6911 nv = 96 ne = 84 npr = 52337 no. pairs analyzed = 52337 no. exposed pairs = 3103 no. arc points = 22440 no. surface atoms = 1049 nbur = 1546 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 386 mr = 3917 m= 1 mr = 55 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 0.3800000 number of dielectric boundary points 3326 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2221 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8296 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1721817E-09 1.2102769E-08 midg,1,midg; midg,igrid,midg 8.8286400E-09 8.4365237E-10 1,midg,midg; igrid,midg,midg -5.5170921E-09 8.3692351E-09 gauss-seidel spectral radius is 0.9867117 estimated iterations to convergence 71 setup time was (sec) 0.7100000 now iterating at: 19:13:06 rms-change max change #iterations 0.1334053 20.25733 at 10iterations 1.2480172E-02 1.789061 at 20iterations 1.1657176E-03 0.1735134 at 30iterations 1.0922574E-04 1.6826630E-02 at 40iterations 1.0700075E-05 1.6756058E-03 at 50iterations finished qdiffx linear iterations at : 19:13:10 total time elapsed so far: 4.290000 # loops : 50 mean,max change (kT/e) : 1.0700075E-05 1.6756058E-03 energy calculations done at 4.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.500000 DelPhi exited at 19:13:10 4.501u 0.420s 0:05.20 94.6% 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 19:13:10 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2595 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 1.872764 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): -32.00200 18.27800 ymin,ymax (A): -24.32800 23.29400 zmin,zma (A): -12.46000 44.56800 x,y,z range (A): 50.28000 47.62200 57.02800 scale (grids/A): 1.872764 object centre (A): -6.862000 -0.5170002 16.05400 number of atom coordinates read : 2595 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 84.99767 87.75613 89.70193 assigned negative charge : -390.0956 centred at (gu) : 84.68476 87.88670 89.37426 start vw surface at 0.1600000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 74146 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22440 grid for indexing accessible points = 1.400000 m= 28094 mr = 51969 m= 4651 mr = 21318 m= 256 mr = 3067 m= 2 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 894 time to turn everything in is 0.7700000 number of dielectric boundary points 30701 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 19324 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) : 0.6242548 object centre at (A) : -6.862000 -0.5170002 16.05400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4455489E-02 2.5979586E-02 midg,1,midg; midg,igrid,midg 1.5141605E-02 2.8557261E-03 1,midg,midg; igrid,midg,midg -4.7200830E-03 3.4845263E-02 gauss-seidel spectral radius is 0.9985938 estimated iterations to convergence 211 setup time was (sec) 1.100000 now iterating at: 19:13:12 rms-change max change #iterations 4.111266 186.4480 at 10iterations 1.907098 63.88412 at 20iterations 0.8800237 29.06667 at 30iterations 0.4067301 13.14948 at 40iterations 0.1888238 6.420124 at 50iterations 8.7383278E-02 3.164239 at 60iterations 4.0380720E-02 1.238457 at 70iterations 1.8695526E-02 0.6246920 at 80iterations 8.6782919E-03 0.2681198 at 90iterations 4.0095085E-03 0.1271191 at 100iterations 1.8659473E-03 5.9524536E-02 at 110iterations 8.6616119E-04 2.8240204E-02 at 120iterations finished qdiffx linear iterations at : 19:13:21 total time elapsed so far: 10.47000 # loops : 120 mean,max change (kT/e) : 8.6616119E-04 2.8240204E-02 energy calculations done at 10.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.69000 DelPhi exited at 19:13:22 10.695u 0.460s 0:11.47 97.2% 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 19:13:22 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2595 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 2.809146 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): -32.00200 18.27800 ymin,ymax (A): -24.32800 23.29400 zmin,zma (A): -12.46000 44.56800 x,y,z range (A): 50.28000 47.62200 57.02800 scale (grids/A): 2.809146 object centre (A): -6.862000 -0.5170002 16.05400 number of atom coordinates read : 2595 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 82.49622 86.63401 89.55278 assigned negative charge : -390.0956 centred at (gu) : 82.02710 86.83002 89.06138 start vw surface at 0.1600000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 170771 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22440 grid for indexing accessible points = 1.400000 m= 89890 mr = 124846 m= 33787 mr = 74789 m= 8572 mr = 27761 m= 1220 mr = 6717 m= 43 mr = 815 m= 0 mr = 15 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 3152 time to turn everything in is 1.970000 number of dielectric boundary points 69340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 19723 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) : 1.872764 object centre at (A) : -6.862000 -0.5170002 16.05400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7126172E-02 0.2774900 midg,1,midg; midg,igrid,midg 0.1914965 2.2636520E-02 1,midg,midg; igrid,midg,midg -4.7500934E-02 0.4247472 gauss-seidel spectral radius is 0.9992453 estimated iterations to convergence 287 setup time was (sec) 2.340000 now iterating at: 19:13:24 rms-change max change #iterations 9.643806 442.1238 at 10iterations 5.566822 125.1224 at 20iterations 3.195869 92.01085 at 30iterations 1.829442 35.23714 at 40iterations 1.048732 21.79483 at 50iterations 0.5991794 11.15779 at 60iterations 0.3423398 5.993740 at 70iterations 0.1958034 3.376072 at 80iterations 0.1113708 1.999443 at 90iterations 6.3684896E-02 1.144433 at 100iterations 3.6411323E-02 0.6786947 at 110iterations 2.0735344E-02 0.3636169 at 120iterations 1.1856752E-02 0.2089539 at 130iterations 6.7596426E-03 0.1271572 at 140iterations 3.8616254E-03 6.8318367E-02 at 150iterations 2.2055539E-03 4.0428162E-02 at 160iterations 1.2581178E-03 2.3145676E-02 at 170iterations 7.1811321E-04 1.2199402E-02 at 180iterations finished qdiffx linear iterations at : 19:13:40 total time elapsed so far: 18.39000 # loops : 180 mean,max change (kT/e) : 7.1811321E-04 1.2199402E-02 energy calculations done at 18.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.61000 DelPhi exited at 19:13:41 18.616u 0.459s 0:19.36 98.4% 0+0k 0+0io 0pf+0w