Mon Oct 10 18:53:05 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 Mon Oct 10 2011 at 18:53:05 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4112 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: 0.5529324 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): -75.47600 -16.08100 ymin,ymax (A): -40.30300 24.08100 zmin,zma (A): 198.2420 257.7090 x,y,z range (A): 59.39500 64.38400 59.46703 scale (grids/A): 0.5529324 object centre (A): -45.77850 -8.110998 227.9755 number of atom coordinates read : 4112 total number of charged atoms : 3963 net assigned charge : 2.500036 assigned positive charge : 632.7567 centred at (gu) : 90.14584 91.97562 87.73343 assigned negative charge : -630.2601 centred at (gu) : 90.22166 91.90571 87.83084 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8219 nv = 96 ne = 84 npr = 81633 no. pairs analyzed = 81633 no. exposed pairs = 5382 no. arc points = 37361 no. surface atoms = 1797 nbur = 2315 mkacc time = 0.2100000 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 = 1.540000 m= 348 mr = 4290 m= 0 mr = 11 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.4400000 number of dielectric boundary points 4266 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3775 ## 499 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 10814 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3201623E-09 -5.8876493E-10 midg,1,midg; midg,igrid,midg -4.2427420E-10 1.6215242E-09 1,midg,midg; igrid,midg,midg 1.0230593E-09 -7.9566131E-10 gauss-seidel spectral radius is 0.9832222 estimated iterations to convergence 64 setup time was (sec) 0.7300000 now iterating at: 18:53:06 rms-change max change #iterations 9.1043442E-02 16.50533 at 10iterations 6.9104503E-03 0.9708405 at 20iterations 1.0963867E-03 0.2569389 at 30iterations 4.3301343E-04 0.1076126 at 40iterations 2.0518448E-04 4.7672272E-02 at 50iterations finished qdiffx linear iterations at : 18:53:10 total time elapsed so far: 4.610000 # loops : 50 mean,max change (kT/e) : 2.0518448E-04 4.7672272E-02 energy calculations done at 4.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.770000 DelPhi exited at 18:53:11 4.777u 0.412s 0:05.66 91.5% 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 18:53:11 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4112 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: 1.658797 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): -75.47600 -16.08100 ymin,ymax (A): -40.30300 24.08100 zmin,zma (A): 198.2420 257.7090 x,y,z range (A): 59.39500 64.38400 59.46703 scale (grids/A): 1.658797 object centre (A): -45.77850 -8.110998 227.9755 number of atom coordinates read : 4112 total number of charged atoms : 3963 net assigned charge : 2.500036 assigned positive charge : 632.7567 centred at (gu) : 90.43624 95.92542 83.19881 assigned negative charge : -630.2601 centred at (gu) : 90.66457 95.71692 83.49230 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 90571 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37361 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 29782 mr = 61917 m= 3409 mr = 20713 m= 105 mr = 1765 m= 0 mr = 5 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 632 time to turn everything in is 0.7500000 number of dielectric boundary points 39467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 425 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 30404 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) : 0.5529324 object centre at (A) : -45.77850 -8.110998 227.9755 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0536788E-03 -1.2842190E-02 midg,1,midg; midg,igrid,midg -1.2115234E-02 2.0931333E-02 1,midg,midg; igrid,midg,midg 1.2331292E-03 3.8828936E-03 gauss-seidel spectral radius is 0.9983544 estimated iterations to convergence 196 setup time was (sec) 1.050000 now iterating at: 18:53:12 rms-change max change #iterations 4.187395 150.2482 at 10iterations 1.820054 59.88564 at 20iterations 0.7936391 25.52757 at 30iterations 0.3454052 11.09839 at 40iterations 0.1506762 4.661266 at 50iterations 6.5652266E-02 2.173090 at 60iterations 2.8708404E-02 0.8678298 at 70iterations 1.2573896E-02 0.3784456 at 80iterations 5.5861901E-03 0.1822605 at 90iterations 2.5738203E-03 9.4024658E-02 at 100iterations 1.2753503E-03 5.3649902E-02 at 110iterations 7.3301711E-04 2.8638840E-02 at 120iterations finished qdiffx linear iterations at : 18:53:22 total time elapsed so far: 10.70000 # loops : 120 mean,max change (kT/e) : 7.3301711E-04 2.8638840E-02 energy calculations done at 10.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.87000 DelPhi exited at 18:53:22 10.874u 0.446s 0:11.67 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 Mon Oct 10 2011 at 18:53:23 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4112 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: 2.488196 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): -75.47600 -16.08100 ymin,ymax (A): -40.30300 24.08100 zmin,zma (A): 198.2420 257.7090 x,y,z range (A): 59.39500 64.38400 59.46703 scale (grids/A): 2.488196 object centre (A): -45.77850 -8.110998 227.9755 number of atom coordinates read : 4112 total number of charged atoms : 3963 net assigned charge : 2.500036 assigned positive charge : 632.7567 centred at (gu) : 90.65408 98.88782 79.79794 assigned negative charge : -630.2601 centred at (gu) : 90.99677 98.57526 80.23837 start vw surface at 0.1600000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 210487 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37361 grid for indexing accessible points = 1.400000 m= 100655 mr = 151785 m= 30634 mr = 79730 m= 5469 mr = 23174 m= 481 mr = 3669 m= 9 mr = 238 m= 0 mr = 0 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 2038 time to turn everything in is 1.900000 number of dielectric boundary points 89139 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 31679 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) : 1.658797 object centre at (A) : -45.77850 -8.110998 227.9755 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3347526E-02 -0.1785851 midg,1,midg; midg,igrid,midg -0.5345979 0.3911333 1,midg,midg; igrid,midg,midg -5.9799254E-02 6.0182087E-02 gauss-seidel spectral radius is 0.9992173 estimated iterations to convergence 282 setup time was (sec) 2.240000 now iterating at: 18:53:25 rms-change max change #iterations 10.85867 362.4128 at 10iterations 6.318556 131.8566 at 20iterations 3.666562 76.90956 at 30iterations 2.110296 45.21756 at 40iterations 1.214033 24.72417 at 50iterations 0.6940981 12.68979 at 60iterations 0.3961202 7.949266 at 70iterations 0.2256686 4.040618 at 80iterations 0.1285451 2.501598 at 90iterations 7.2991252E-02 1.264837 at 100iterations 4.1529659E-02 0.8240681 at 110iterations 2.3647126E-02 0.4137983 at 120iterations 1.3455480E-02 0.2359047 at 130iterations 7.6697730E-03 0.1475925 at 140iterations 4.3818234E-03 8.3236694E-02 at 150iterations 2.5223109E-03 4.9118042E-02 at 160iterations 1.4923208E-03 3.5072327E-02 at 170iterations 9.0907962E-04 2.0755768E-02 at 180iterations finished qdiffx linear iterations at : 18:53:42 total time elapsed so far: 19.01000 # loops : 180 mean,max change (kT/e) : 9.0907962E-04 2.0755768E-02 energy calculations done at 19.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.18000 DelPhi exited at 18:53:43 19.181u 0.483s 0:20.02 98.2% 0+0k 0+0io 0pf+0w