Mon Oct 10 17:01:43 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 17:01:43 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2792 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6182488 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): 13.83800 71.42000 ymin,ymax (A): 4.104000 51.29600 zmin,zma (A): 6.763000 62.39900 x,y,z range (A): 57.58200 47.19200 55.63600 scale (grids/A): 0.6182488 object centre (A): 42.62900 27.70000 34.58100 number of atom coordinates read : 2792 total number of charged atoms : 2651 net assigned charge : 1.4032640E-02 assigned positive charge : 421.7043 centred at (gu) : 88.76823 90.28867 91.12113 assigned negative charge : -421.6914 centred at (gu) : 88.62763 90.39535 91.13908 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7279 nv = 96 ne = 84 npr = 54614 no. pairs analyzed = 54614 no. exposed pairs = 3734 no. arc points = 26793 no. surface atoms = 1264 nbur = 1528 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 363 mr = 3704 m= 0 mr = 32 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3906 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2702 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8826 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1047100E-09 -1.3356237E-09 midg,1,midg; midg,igrid,midg 6.9400414E-09 -7.6757258E-09 1,midg,midg; igrid,midg,midg -1.2669220E-08 7.3385977E-09 gauss-seidel spectral radius is 0.9864807 estimated iterations to convergence 70 setup time was (sec) 0.6400000 now iterating at: 17:01:44 rms-change max change #iterations 0.1271270 20.47668 at 10iterations 1.1589286E-02 1.640499 at 20iterations 1.0462122E-03 0.1564026 at 30iterations 9.6798867E-05 1.4139652E-02 at 40iterations 9.0157446E-06 1.1711121E-03 at 50iterations finished qdiffx linear iterations at : 17:01:47 total time elapsed so far: 4.020000 # loops : 50 mean,max change (kT/e) : 9.0157446E-06 1.1711121E-03 energy calculations done at 4.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 17:01:49 4.203u 0.283s 0:05.67 79.0% 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 17:01:49 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2792 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.854746 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): 13.83800 71.42000 ymin,ymax (A): 4.104000 51.29600 zmin,zma (A): 6.763000 62.39900 x,y,z range (A): 57.58200 47.19200 55.63600 scale (grids/A): 1.854746 object centre (A): 42.62900 27.70000 34.58100 number of atom coordinates read : 2792 total number of charged atoms : 2651 net assigned charge : 1.4032640E-02 assigned positive charge : 421.7043 centred at (gu) : 86.30392 90.86519 93.36288 assigned negative charge : -421.6914 centred at (gu) : 85.88261 91.18593 93.41654 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 78882 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26793 grid for indexing accessible points = 1.400000 m= 26731 mr = 52765 m= 3667 mr = 18686 m= 172 mr = 2060 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 1013 time to turn everything in is 0.6900000 number of dielectric boundary points 35894 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 194 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 20851 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) : 0.6182488 object centre at (A) : 42.62900 27.70000 34.58100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.3394079E-03 6.7930506E-03 midg,1,midg; midg,igrid,midg 8.9297527E-03 -1.3760511E-02 1,midg,midg; igrid,midg,midg -5.3601570E-02 2.9874485E-02 gauss-seidel spectral radius is 0.9985963 estimated iterations to convergence 212 setup time was (sec) 0.9900000 now iterating at: 17:01:50 rms-change max change #iterations 4.212597 183.0995 at 10iterations 1.946785 83.41685 at 20iterations 0.9000858 27.67670 at 30iterations 0.4164164 14.00474 at 40iterations 0.1919680 6.139450 at 50iterations 8.8554479E-02 2.880473 at 60iterations 4.1000694E-02 1.298927 at 70iterations 1.9043935E-02 0.6538553 at 80iterations 8.7672221E-03 0.2753038 at 90iterations 4.0648719E-03 0.1261711 at 100iterations 1.8805485E-03 5.6366920E-02 at 110iterations 8.6832209E-04 2.7137756E-02 at 120iterations finished qdiffx linear iterations at : 17:01:59 total time elapsed so far: 9.490000 # loops : 120 mean,max change (kT/e) : 8.6832209E-04 2.7137756E-02 energy calculations done at 9.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.670000 DelPhi exited at 17:02:01 9.669u 0.349s 0:11.87 84.2% 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 Mon Oct 10 2011 at 17:02:01 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2792 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.782120 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): 13.83800 71.42000 ymin,ymax (A): 4.104000 51.29600 zmin,zma (A): 6.763000 62.39900 x,y,z range (A): 57.58200 47.19200 55.63600 scale (grids/A): 2.782120 object centre (A): 42.62900 27.70000 34.58100 number of atom coordinates read : 2792 total number of charged atoms : 2651 net assigned charge : 1.4032640E-02 assigned positive charge : 421.7043 centred at (gu) : 84.45556 91.29758 95.04404 assigned negative charge : -421.6914 centred at (gu) : 83.82389 91.77874 95.12480 start vw surface at 0.1700000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 182300 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26793 grid for indexing accessible points = 1.400000 m= 87521 mr = 128434 m= 29396 mr = 69658 m= 6496 mr = 22596 m= 802 mr = 4523 m= 44 mr = 473 m= 0 mr = 9 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 3540 time to turn everything in is 1.780000 number of dielectric boundary points 80866 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 21205 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) : 1.854746 object centre at (A) : 42.62900 27.70000 34.58100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8287768E-02 0.1860172 midg,1,midg; midg,igrid,midg 6.9424324E-02 -9.7715087E-02 1,midg,midg; igrid,midg,midg -0.6657909 0.3792808 gauss-seidel spectral radius is 0.9992713 estimated iterations to convergence 292 setup time was (sec) 2.130000 now iterating at: 17:02:03 rms-change max change #iterations 10.38163 346.4361 at 10iterations 6.200054 143.3443 at 20iterations 3.662680 82.88867 at 30iterations 2.151627 49.83991 at 40iterations 1.258399 31.36788 at 50iterations 0.7327557 15.11551 at 60iterations 0.4263213 8.494166 at 70iterations 0.2475805 4.770634 at 80iterations 0.1432118 3.292736 at 90iterations 8.2983129E-02 1.554861 at 100iterations 4.7990717E-02 0.8929759 at 110iterations 2.7746938E-02 0.4779949 at 120iterations 1.6045818E-02 0.3065166 at 130iterations 9.2786187E-03 0.1817608 at 140iterations 5.3455783E-03 9.9582672E-02 at 150iterations 3.0930683E-03 5.8450513E-02 at 160iterations 1.7838036E-03 3.1768799E-02 at 170iterations 1.0322571E-03 1.9340515E-02 at 180iterations finished qdiffx linear iterations at : 17:02:18 total time elapsed so far: 16.43000 # loops : 180 mean,max change (kT/e) : 1.0322571E-03 1.9340515E-02 energy calculations done at 16.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.60000 DelPhi exited at 17:02:19 16.602u 0.334s 0:18.22 92.9% 0+0k 0+0io 0pf+0w