Mon Oct 10 17:01:05 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+sph.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 = amb.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 17:01:05 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4482 !!! WARNING: HEM 821 has a net charge of 1.4000 !!! WARNING: ZN8 822 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5100871 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): -16.68600 37.47000 ymin,ymax (A): -33.25100 32.75300 zmin,zma (A): -4.230000 65.56200 x,y,z range (A): 54.15600 66.00400 69.79200 scale (grids/A): 0.5100871 object centre (A): 10.39200 -0.2489986 30.66600 number of atom coordinates read : 4482 total number of charged atoms : 4238 net assigned charge : 4.700031 assigned positive charge : 667.1158 centred at (gu) : 90.16805 91.10796 87.53558 assigned negative charge : -662.4201 centred at (gu) : 90.03332 91.13077 87.55916 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 7457 nv = 96 ne = 84 npr = 90510 no. pairs analyzed = 90510 no. exposed pairs = 5813 no. arc points = 40590 no. surface atoms = 1929 nbur = 2553 mkacc time = 0.2200000 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 = 1.680000 m= 258 mr = 3764 m= 0 mr = 11 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 3940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3877 ## 604 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 9894 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2718517E-10 5.2212141E-12 midg,1,midg; midg,igrid,midg 8.7250318E-11 1.2306995E-11 1,midg,midg; igrid,midg,midg -2.4510455E-10 3.8879880E-10 gauss-seidel spectral radius is 0.9803274 estimated iterations to convergence 59 setup time was (sec) 0.7300000 now iterating at: 17:01:06 rms-change max change #iterations 6.5315172E-02 9.778419 at 10iterations 3.9326707E-03 0.5888017 at 20iterations 5.8439543E-04 7.6257229E-02 at 30iterations 2.0096645E-04 2.5735863E-02 at 40iterations 7.4063624E-05 1.0560930E-02 at 50iterations finished qdiffx linear iterations at : 17:01:08 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 7.4063624E-05 1.0560930E-02 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 17:01:10 3.649u 0.173s 0:05.50 69.2% 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 17:01:10 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4482 !!! WARNING: HEM 821 has a net charge of 1.4000 !!! WARNING: ZN8 822 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.530261 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): -16.68600 37.47000 ymin,ymax (A): -33.25100 32.75300 zmin,zma (A): -4.230000 65.56200 x,y,z range (A): 54.15600 66.00400 69.79200 scale (grids/A): 1.530261 object centre (A): 10.39200 -0.2489986 30.66600 number of atom coordinates read : 4482 total number of charged atoms : 4238 net assigned charge : 4.700031 assigned positive charge : 667.1158 centred at (gu) : 90.50280 93.32240 82.60519 assigned negative charge : -662.4201 centred at (gu) : 90.09975 93.39197 82.67723 start vw surface at 0.2200000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 84583 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40590 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23830 mr = 57734 m= 1956 mr = 15267 m= 46 mr = 805 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 258 time to turn everything in is 0.6400000 number of dielectric boundary points 36609 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 472 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 31819 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) : 0.5100871 object centre at (A) : 10.39200 -0.2489986 30.66600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6766591E-03 9.5477402E-03 midg,1,midg; midg,igrid,midg 1.7717835E-03 -5.0322069E-03 1,midg,midg; igrid,midg,midg -3.7792805E-03 9.2439558E-03 gauss-seidel spectral radius is 0.9980817 estimated iterations to convergence 181 setup time was (sec) 0.9300000 now iterating at: 17:01:11 rms-change max change #iterations 3.626972 151.3619 at 10iterations 1.470758 52.02619 at 20iterations 0.5980064 20.72312 at 30iterations 0.2430526 8.094113 at 40iterations 9.9246010E-02 3.263126 at 50iterations 4.0431239E-02 1.260910 at 60iterations 1.6529830E-02 0.6408920 at 70iterations 6.8243998E-03 0.2203026 at 80iterations 2.8499763E-03 0.1010895 at 90iterations 1.2310394E-03 4.0671825E-02 at 100iterations 5.7664711E-04 2.1904945E-02 at 110iterations 3.0494947E-04 1.0139942E-02 at 120iterations finished qdiffx linear iterations at : 17:01:18 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 3.0494947E-04 1.0139942E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 17:01:19 8.001u 0.171s 0:09.28 88.0% 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 17:01:20 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4482 !!! WARNING: HEM 821 has a net charge of 1.4000 !!! WARNING: ZN8 822 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.295392 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): -16.68600 37.47000 ymin,ymax (A): -33.25100 32.75300 zmin,zma (A): -4.230000 65.56200 x,y,z range (A): 54.15600 66.00400 69.79200 scale (grids/A): 2.295392 object centre (A): 10.39200 -0.2489986 30.66600 number of atom coordinates read : 4482 total number of charged atoms : 4238 net assigned charge : 4.700031 assigned positive charge : 667.1158 centred at (gu) : 90.75383 94.98331 78.90736 assigned negative charge : -662.4201 centred at (gu) : 90.14948 95.08776 79.01597 start vw surface at 0.2000000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 197439 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40590 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 86204 mr = 142157 m= 20801 mr = 66473 m= 2795 mr = 14402 m= 146 mr = 1635 m= 3 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 833 time to turn everything in is 1.520000 number of dielectric boundary points 82671 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 33817 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) : 1.530261 object centre at (A) : 10.39200 -0.2489986 30.66600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1435942 0.2690232 midg,1,midg; midg,igrid,midg 1.9227821E-02 -0.2310757 1,midg,midg; igrid,midg,midg -3.7710574E-02 0.1233116 gauss-seidel spectral radius is 0.9991488 estimated iterations to convergence 271 setup time was (sec) 1.840000 now iterating at: 17:01:22 rms-change max change #iterations 9.833586 267.6880 at 10iterations 5.600095 137.5164 at 20iterations 3.161650 76.26906 at 30iterations 1.779041 39.07590 at 40iterations 0.9998026 27.60683 at 50iterations 0.5581902 12.55753 at 60iterations 0.3109255 6.785288 at 70iterations 0.1728268 3.406761 at 80iterations 9.6284956E-02 1.970906 at 90iterations 5.3447023E-02 1.297169 at 100iterations 2.9663842E-02 0.6265335 at 110iterations 1.6431816E-02 0.3317208 at 120iterations 9.1089737E-03 0.1904221 at 130iterations 5.0515742E-03 0.1053467 at 140iterations 2.8060207E-03 5.5858612E-02 at 150iterations 1.5665876E-03 3.4202576E-02 at 160iterations 8.7540247E-04 1.7413378E-02 at 170iterations 4.9599964E-04 1.0234192E-02 at 180iterations finished qdiffx linear iterations at : 17:01:33 total time elapsed so far: 13.32000 # loops : 180 mean,max change (kT/e) : 4.9599964E-04 1.0234192E-02 energy calculations done at 13.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.51000 DelPhi exited at 17:01:34 13.508u 0.264s 0:14.44 95.2% 0+0k 0+0io 0pf+0w