Tue Oct 11 08:29:25 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 Tue Oct 11 2011 at 08:29:25 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4144 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5317640 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): -30.81100 30.15000 ymin,ymax (A): -24.27300 37.05900 zmin,zma (A): -38.70300 28.24400 x,y,z range (A): 60.96100 61.33200 66.94700 scale (grids/A): 0.5317640 object centre (A): -0.3304996 6.393002 -5.229500 number of atom coordinates read : 4144 total number of charged atoms : 4001 net assigned charge : -0.4999611 assigned positive charge : 624.0770 centred at (gu) : 87.57350 90.03059 90.48103 assigned negative charge : -624.5803 centred at (gu) : 87.56789 90.15385 90.50960 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7656 nv = 96 ne = 84 npr = 82280 no. pairs analyzed = 82280 no. exposed pairs = 5477 no. arc points = 38362 no. surface atoms = 1822 nbur = 2322 mkacc time = 0.2000000 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 = 1.624000 m= 306 mr = 3805 m= 0 mr = 3 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3986 ## 577 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 10160 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2147502E-10 -1.9141022E-10 midg,1,midg; midg,igrid,midg 6.3087363E-10 -6.9276601E-10 1,midg,midg; igrid,midg,midg -8.4591015E-11 7.7548757E-12 gauss-seidel spectral radius is 0.9818750 estimated iterations to convergence 61 setup time was (sec) 0.6600000 now iterating at: 08:29:26 rms-change max change #iterations 7.7663772E-02 12.40148 at 10iterations 4.9458854E-03 0.6629467 at 20iterations 3.9475886E-04 6.8400383E-02 at 30iterations 7.7627643E-05 1.2240767E-02 at 40iterations 2.2499309E-05 3.5972595E-03 at 50iterations finished qdiffx linear iterations at : 08:29:28 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 2.2499309E-05 3.5972595E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 08:29:29 3.472u 0.149s 0:03.93 91.8% 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 Tue Oct 11 2011 at 08:29:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4144 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.595292 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): -30.81100 30.15000 ymin,ymax (A): -24.27300 37.05900 zmin,zma (A): -38.70300 28.24400 x,y,z range (A): 60.96100 61.33200 66.94700 scale (grids/A): 1.595292 object centre (A): -0.3304996 6.393002 -5.229500 number of atom coordinates read : 4144 total number of charged atoms : 4001 net assigned charge : -0.4999611 assigned positive charge : 624.0770 centred at (gu) : 82.71888 90.09021 91.44153 assigned negative charge : -624.5803 centred at (gu) : 82.70313 90.46107 91.52817 start vw surface at 0.2200000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 84643 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38362 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 25452 mr = 55863 m= 2285 mr = 16896 m= 53 mr = 947 m= 0 mr = 1 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 112 time to turn everything in is 0.6600000 number of dielectric boundary points 38726 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 528 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 30460 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) : 0.5317640 object centre at (A) : -0.3304996 6.393002 -5.229500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5119501E-03 -7.1643200E-03 midg,1,midg; midg,igrid,midg 7.4087796E-03 -1.3376224E-02 1,midg,midg; igrid,midg,midg 1.7244156E-02 8.5577741E-03 gauss-seidel spectral radius is 0.9982261 estimated iterations to convergence 189 setup time was (sec) 0.9500000 now iterating at: 08:29:30 rms-change max change #iterations 3.809408 150.1423 at 10iterations 1.596226 59.83661 at 20iterations 0.6723431 22.37447 at 30iterations 0.2833736 9.624079 at 40iterations 0.1187030 3.952919 at 50iterations 5.0125636E-02 1.496380 at 60iterations 2.1046268E-02 0.6815147 at 70iterations 8.8996366E-03 0.2985289 at 80iterations 3.7559739E-03 0.1234859 at 90iterations 1.5820987E-03 5.5088043E-02 at 100iterations 6.7082496E-04 2.1060944E-02 at 110iterations 2.8585189E-04 9.6130371E-03 at 120iterations finished qdiffx linear iterations at : 08:29:36 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 2.8585189E-04 9.6130371E-03 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 08:29:37 7.660u 0.157s 0:08.31 93.9% 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 Tue Oct 11 2011 at 08:29:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4144 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.392938 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): -30.81100 30.15000 ymin,ymax (A): -24.27300 37.05900 zmin,zma (A): -38.70300 28.24400 x,y,z range (A): 60.96100 61.33200 66.94700 scale (grids/A): 2.392938 object centre (A): -0.3304996 6.393002 -5.229500 number of atom coordinates read : 4144 total number of charged atoms : 4001 net assigned charge : -0.4999611 assigned positive charge : 624.0770 centred at (gu) : 79.07806 90.13488 92.16190 assigned negative charge : -624.5803 centred at (gu) : 79.05456 90.69153 92.29212 start vw surface at 0.1900000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 196383 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38362 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 89346 mr = 137152 m= 23954 mr = 69310 m= 3332 mr = 17419 m= 194 mr = 1899 m= 3 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 356 time to turn everything in is 1.510000 number of dielectric boundary points 87382 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 42 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 31942 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) : 1.595292 object centre at (A) : -0.3304996 6.393002 -5.229500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2770720 -0.1875704 midg,1,midg; midg,igrid,midg 9.0801515E-02 -0.1787994 1,midg,midg; igrid,midg,midg 0.2404622 7.4358135E-02 gauss-seidel spectral radius is 0.9991895 estimated iterations to convergence 277 setup time was (sec) 1.810000 now iterating at: 08:29:39 rms-change max change #iterations 10.16989 307.3306 at 10iterations 5.908935 138.8189 at 20iterations 3.411499 76.15889 at 30iterations 1.950910 41.34082 at 40iterations 1.110813 24.01006 at 50iterations 0.6305199 14.07156 at 60iterations 0.3573704 6.655424 at 70iterations 0.2014003 3.856266 at 80iterations 0.1138062 2.222976 at 90iterations 6.4097866E-02 1.224514 at 100iterations 3.6130890E-02 0.6892900 at 110iterations 2.0275479E-02 0.3778677 at 120iterations 1.1399949E-02 0.2229557 at 130iterations 6.3925865E-03 0.1225822 at 140iterations 3.6006738E-03 7.1804047E-02 at 150iterations 2.0210398E-03 4.0594101E-02 at 160iterations 1.1399944E-03 1.9969940E-02 at 170iterations 6.4162724E-04 1.1596680E-02 at 180iterations finished qdiffx linear iterations at : 08:29:49 total time elapsed so far: 12.18000 # loops : 180 mean,max change (kT/e) : 6.4162724E-04 1.1596680E-02 energy calculations done at 12.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.38000 DelPhi exited at 08:29:50 12.383u 0.174s 0:13.11 95.7% 0+0k 0+0io 0pf+0w