Sun Oct 9 07:54:39 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 Sun Oct 9 2011 at 07:54:39 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: NAP 207 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7084154 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): -16.38500 30.93800 ymin,ymax (A): -20.06200 30.19100 zmin,zma (A): -4.569000 35.06000 x,y,z range (A): 47.32300 50.25300 39.62900 scale (grids/A): 0.7084154 object centre (A): 7.276500 5.064500 15.24550 number of atom coordinates read : 2220 total number of charged atoms : 2083 net assigned charge : 6.000018 assigned positive charge : 334.5084 centred at (gu) : 89.69706 90.79313 90.83434 assigned negative charge : -328.5089 centred at (gu) : 89.58331 90.88485 90.96526 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7615 nv = 96 ne = 84 npr = 45669 no. pairs analyzed = 45669 no. exposed pairs = 2788 no. arc points = 19886 no. surface atoms = 937 nbur = 1283 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 563 mr = 4247 m= 3 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 126 time to turn everything in is 0.2500000 number of dielectric boundary points 3814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1767 ## 167 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 8365 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0364855E-07 -2.1098383E-08 midg,1,midg; midg,igrid,midg 8.7071875E-08 4.0724322E-09 1,midg,midg; igrid,midg,midg -8.6749052E-09 1.0646427E-07 gauss-seidel spectral radius is 0.9896336 estimated iterations to convergence 80 setup time was (sec) 0.4800000 now iterating at: 07:54:40 rms-change max change #iterations 0.2153817 32.20639 at 10iterations 2.6642263E-02 3.317900 at 20iterations 3.2511612E-03 0.4361839 at 30iterations 4.0836624E-04 5.0964355E-02 at 40iterations 4.8948521E-05 6.4659119E-03 at 50iterations finished qdiffx linear iterations at : 07:54:42 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 4.8948521E-05 6.4659119E-03 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 07:54:43 3.260u 0.210s 0:03.75 92.5% 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 Sun Oct 9 2011 at 07:54:43 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: NAP 207 has a net charge of -2.0000 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: 2.125246 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): -16.38500 30.93800 ymin,ymax (A): -20.06200 30.19100 zmin,zma (A): -4.569000 35.06000 x,y,z range (A): 47.32300 50.25300 39.62900 scale (grids/A): 2.125246 object centre (A): 7.276500 5.064500 15.24550 number of atom coordinates read : 2220 total number of charged atoms : 2083 net assigned charge : 6.000018 assigned positive charge : 334.5084 centred at (gu) : 89.09083 92.37901 92.50270 assigned negative charge : -328.5089 centred at (gu) : 88.74983 92.65459 92.89571 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 79215 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19886 grid for indexing accessible points = 1.400000 m= 32139 mr = 54255 m= 7008 mr = 24505 m= 733 mr = 4889 m= 20 mr = 390 m= 0 mr = 2 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 2981 time to turn everything in is 0.6000000 number of dielectric boundary points 35074 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 16552 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) : 0.7084154 object centre at (A) : 7.276500 5.064500 15.24550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1572214E-02 1.2319322E-02 midg,1,midg; midg,igrid,midg 3.2742623E-02 1.3206042E-02 1,midg,midg; igrid,midg,midg -1.8719181E-02 4.2659719E-02 gauss-seidel spectral radius is 0.9988551 estimated iterations to convergence 234 setup time was (sec) 0.8900000 now iterating at: 07:54:44 rms-change max change #iterations 4.826629 189.9255 at 10iterations 2.387178 85.03800 at 20iterations 1.193221 36.46374 at 30iterations 0.5958142 19.51007 at 40iterations 0.2956205 9.254719 at 50iterations 0.1477091 4.334805 at 60iterations 7.3593296E-02 2.402840 at 70iterations 3.6897898E-02 1.076546 at 80iterations 1.8333241E-02 0.4989719 at 90iterations 9.1391308E-03 0.2769413 at 100iterations 4.5643500E-03 0.1301351 at 110iterations 2.2770546E-03 6.7190170E-02 at 120iterations finished qdiffx linear iterations at : 07:54:51 total time elapsed so far: 8.210000 # loops : 120 mean,max change (kT/e) : 2.2770546E-03 6.7190170E-02 energy calculations done at 8.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.400000 DelPhi exited at 07:54:52 8.403u 0.208s 0:08.87 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 Sun Oct 9 2011 at 07:54:52 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: NAP 207 has a net charge of -2.0000 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: 3.187870 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): -16.38500 30.93800 ymin,ymax (A): -20.06200 30.19100 zmin,zma (A): -4.569000 35.06000 x,y,z range (A): 47.32300 50.25300 39.62900 scale (grids/A): 3.187870 object centre (A): 7.276500 5.064500 15.24550 number of atom coordinates read : 2220 total number of charged atoms : 2083 net assigned charge : 6.000018 assigned positive charge : 334.5084 centred at (gu) : 88.63613 93.56844 93.75397 assigned negative charge : -328.5089 centred at (gu) : 88.12474 93.98188 94.34361 start vw surface at 0.1400000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 182448 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19886 grid for indexing accessible points = 1.400000 m= 97966 mr = 130837 m= 42547 mr = 81212 m= 13378 mr = 35478 m= 2855 mr = 10576 m= 377 mr = 2167 m= 30 mr = 272 m= 0 mr = 7 time to grow re-entrant surface = 0.8899999 no. cavity mid-points inaccessible to solvent = 10005 time to turn everything in is 1.840000 number of dielectric boundary points 79052 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 16664 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) : 2.125246 object centre at (A) : 7.276500 5.064500 15.24550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6437194 0.1078047 midg,1,midg; midg,igrid,midg 0.2842092 0.2713612 1,midg,midg; igrid,midg,midg -8.7439112E-02 0.3293243 gauss-seidel spectral radius is 0.9992990 estimated iterations to convergence 298 setup time was (sec) 2.150000 now iterating at: 07:54:54 rms-change max change #iterations 10.57992 348.1626 at 10iterations 6.162018 114.7565 at 20iterations 3.588351 65.77027 at 30iterations 2.088738 39.41054 at 40iterations 1.220396 23.21404 at 50iterations 0.7085549 12.63370 at 60iterations 0.4124269 7.238411 at 70iterations 0.2398083 4.188307 at 80iterations 0.1393706 2.358078 at 90iterations 8.1442989E-02 1.357592 at 100iterations 4.7226537E-02 0.7595425 at 110iterations 2.7510738E-02 0.4546072 at 120iterations 1.6032288E-02 0.2909203 at 130iterations 9.3681877E-03 0.1534131 at 140iterations 5.4308651E-03 9.1661453E-02 at 150iterations 3.1653433E-03 5.5721283E-02 at 160iterations 1.8409360E-03 3.1330109E-02 at 170iterations 1.0752035E-03 1.8114090E-02 at 180iterations finished qdiffx linear iterations at : 07:55:05 total time elapsed so far: 12.55000 # loops : 180 mean,max change (kT/e) : 1.0752035E-03 1.8114090E-02 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.73000 DelPhi exited at 07:55:05 12.730u 0.225s 0:13.22 97.9% 0+0k 0+0io 0pf+0w