Mon Oct 10 10:37:16 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 10:37:16 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2880 !!! WARNING: HIT 232 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: 0.5652409 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): 19.44400 82.42600 ymin,ymax (A): 31.05600 86.63800 zmin,zma (A): -1.633000 50.74600 x,y,z range (A): 62.98200 55.58200 52.37900 scale (grids/A): 0.5652409 object centre (A): 50.93500 58.84700 24.55650 number of atom coordinates read : 2880 total number of charged atoms : 2729 net assigned charge : 7.014019 assigned positive charge : 423.9488 centred at (gu) : 87.61728 89.20781 86.74790 assigned negative charge : -416.9353 centred at (gu) : 87.52328 89.16032 86.63235 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6252 nv = 96 ne = 84 npr = 55641 no. pairs analyzed = 55641 no. exposed pairs = 4255 no. arc points = 30402 no. surface atoms = 1408 nbur = 1472 mkacc time = 0.1500000 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 = 1.512000 m= 271 mr = 2809 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2974 ## 337 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7904 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1011118E-09 1.1027016E-09 midg,1,midg; midg,igrid,midg 4.6641435E-10 1.2869705E-09 1,midg,midg; igrid,midg,midg -3.7990722E-10 1.2038028E-09 gauss-seidel spectral radius is 0.9838600 estimated iterations to convergence 65 setup time was (sec) 0.6200000 now iterating at: 10:37:17 rms-change max change #iterations 8.6734429E-02 15.59713 at 10iterations 6.2880521E-03 0.9400892 at 20iterations 4.7094576E-04 7.6117516E-02 at 30iterations 4.3887161E-05 6.2065125E-03 at 40iterations 6.5727440E-06 7.0571899E-04 at 50iterations finished qdiffx linear iterations at : 10:37:20 total time elapsed so far: 4.370000 # loops : 50 mean,max change (kT/e) : 6.5727440E-06 7.0571899E-04 energy calculations done at 4.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.530000 DelPhi exited at 10:37:21 4.530u 0.416s 0:05.21 94.8% 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 Mon Oct 10 2011 at 10:37:21 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2880 !!! WARNING: HIT 232 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: 1.695723 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): 19.44400 82.42600 ymin,ymax (A): 31.05600 86.63800 zmin,zma (A): -1.633000 50.74600 x,y,z range (A): 62.98200 55.58200 52.37900 scale (grids/A): 1.695723 object centre (A): 50.93500 58.84700 24.55650 number of atom coordinates read : 2880 total number of charged atoms : 2729 net assigned charge : 7.014019 assigned positive charge : 423.9488 centred at (gu) : 82.85136 87.62283 80.24339 assigned negative charge : -416.9353 centred at (gu) : 82.56951 87.48106 79.89680 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 68340 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30402 grid for indexing accessible points = 1.400000 m= 20958 mr = 43241 m= 2415 mr = 13350 m= 93 mr = 964 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 34244 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 246 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 21068 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) : 0.5652409 object centre at (A) : 50.93500 58.84700 24.55650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1413010E-03 6.7008482E-03 midg,1,midg; midg,igrid,midg 5.0447336E-03 1.5643250E-02 1,midg,midg; igrid,midg,midg 4.8336000E-03 -3.6534404E-03 gauss-seidel spectral radius is 0.9983191 estimated iterations to convergence 194 setup time was (sec) 0.8800000 now iterating at: 10:37:22 rms-change max change #iterations 3.478155 183.0953 at 10iterations 1.488158 54.07381 at 20iterations 0.6401703 22.83795 at 30iterations 0.2737234 9.674033 at 40iterations 0.1178533 4.193239 at 50iterations 5.0583955E-02 1.749725 at 60iterations 2.1779625E-02 0.8739319 at 70iterations 9.3470365E-03 0.3191051 at 80iterations 4.0299818E-03 0.1480942 at 90iterations 1.7313734E-03 6.2026024E-02 at 100iterations 7.4615702E-04 2.8137207E-02 at 110iterations 3.2108888E-04 1.1554241E-02 at 120iterations finished qdiffx linear iterations at : 10:37:32 total time elapsed so far: 10.69000 # loops : 120 mean,max change (kT/e) : 3.2108888E-04 1.1554241E-02 energy calculations done at 10.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.87000 DelPhi exited at 10:37:32 10.870u 0.436s 0:11.57 97.6% 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 10:37:33 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2880 !!! WARNING: HIT 232 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: 2.543584 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): 19.44400 82.42600 ymin,ymax (A): 31.05600 86.63800 zmin,zma (A): -1.633000 50.74600 x,y,z range (A): 62.98200 55.58200 52.37900 scale (grids/A): 2.543584 object centre (A): 50.93500 58.84700 24.55650 number of atom coordinates read : 2880 total number of charged atoms : 2729 net assigned charge : 7.014019 assigned positive charge : 423.9488 centred at (gu) : 79.27685 86.43404 75.36494 assigned negative charge : -416.9353 centred at (gu) : 78.85422 86.22139 74.84517 start vw surface at 0.1300000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 158591 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30402 grid for indexing accessible points = 1.400000 m= 71268 mr = 107048 m= 21177 mr = 53583 m= 3717 mr = 14826 m= 316 mr = 2095 m= 3 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 0.8899999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.470000 number of dielectric boundary points 77378 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 21818 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) : 1.695723 object centre at (A) : 50.93500 58.84700 24.55650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3455451E-02 7.1308494E-02 midg,1,midg; midg,igrid,midg -2.5267035E-02 0.2220947 1,midg,midg; igrid,midg,midg 0.1396960 4.3124732E-02 gauss-seidel spectral radius is 0.9991845 estimated iterations to convergence 277 setup time was (sec) 1.880000 now iterating at: 10:37:35 rms-change max change #iterations 9.125241 271.1104 at 10iterations 5.305368 169.6055 at 20iterations 3.041003 80.40965 at 30iterations 1.736370 51.79669 at 40iterations 0.9812472 27.88229 at 50iterations 0.5568767 14.50058 at 60iterations 0.3138143 8.438778 at 70iterations 0.1764422 3.902676 at 80iterations 9.9064074E-02 2.007782 at 90iterations 5.5455443E-02 1.406682 at 100iterations 3.1190261E-02 0.6630974 at 110iterations 1.7468270E-02 0.5326834 at 120iterations 9.7750667E-03 0.2023473 at 130iterations 5.4608271E-03 0.1269341 at 140iterations 3.0640834E-03 6.8270206E-02 at 150iterations 1.7091787E-03 3.3901215E-02 at 160iterations 9.5626619E-04 2.0400047E-02 at 170iterations 5.3484732E-04 1.1338234E-02 at 180iterations finished qdiffx linear iterations at : 10:37:53 total time elapsed so far: 19.64000 # loops : 180 mean,max change (kT/e) : 5.3484732E-04 1.1338234E-02 energy calculations done at 19.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.81000 DelPhi exited at 10:37:53 19.816u 0.460s 0:20.54 98.6% 0+0k 0+0io 0pf+0w