Sat Oct 8 17:15:43 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+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 Sat Oct 8 2011 at 17:15:44 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 = 3366 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5548629 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): 37.17600 95.02299 ymin,ymax (A): 16.70400 80.86400 zmin,zma (A): -22.67200 26.68000 x,y,z range (A): 57.84699 64.16000 49.35200 scale (grids/A): 0.5548629 object centre (A): 66.09950 48.78400 2.004001 number of atom coordinates read : 3366 total number of charged atoms : 3220 net assigned charge : -6.499982 assigned positive charge : 503.9186 centred at (gu) : 89.91425 90.08638 89.61471 assigned negative charge : -510.4198 centred at (gu) : 89.92898 90.06377 89.59156 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6816 nv = 96 ne = 84 npr = 67460 no. pairs analyzed = 67460 no. exposed pairs = 4220 no. arc points = 29082 no. surface atoms = 1422 nbur = 1944 mkacc time = 0.1400000 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 = 1.568000 m= 302 mr = 3692 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3404 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2892 ## 368 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8791 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.9463736E-10 -2.9796166E-10 midg,1,midg; midg,igrid,midg -7.9315338E-10 -3.3741254E-10 1,midg,midg; igrid,midg,midg -4.2231213E-10 -7.1110767E-10 gauss-seidel spectral radius is 0.9832776 estimated iterations to convergence 64 setup time was (sec) 0.5500000 now iterating at: 17:15:44 rms-change max change #iterations 8.4910840E-02 12.79627 at 10iterations 6.0036457E-03 0.9522538 at 20iterations 4.8422752E-04 7.8934669E-02 at 30iterations 6.3167805E-05 1.4371872E-02 at 40iterations 1.3621417E-05 3.1023026E-03 at 50iterations finished qdiffx linear iterations at : 17:15:47 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 1.3621417E-05 3.1023026E-03 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 17:15:47 3.162u 0.146s 0:03.57 92.4% 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 Sat Oct 8 2011 at 17:15:47 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 = 3366 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: 1.664589 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): 37.17600 95.02299 ymin,ymax (A): 16.70400 80.86400 zmin,zma (A): -22.67200 26.68000 x,y,z range (A): 57.84699 64.16000 49.35200 scale (grids/A): 1.664589 object centre (A): 66.09950 48.78400 2.004001 number of atom coordinates read : 3366 total number of charged atoms : 3220 net assigned charge : -6.499982 assigned positive charge : 503.9186 centred at (gu) : 89.74191 90.25815 88.84324 assigned negative charge : -510.4198 centred at (gu) : 89.78654 90.19096 88.77418 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75301 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29082 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 25034 mr = 52402 m= 2973 mr = 17803 m= 105 mr = 1605 m= 0 mr = 14 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 31589 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 326 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 24727 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) : 0.5548629 object centre at (A) : 66.09950 48.78400 2.004001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1330491E-03 -4.8097698E-03 midg,1,midg; midg,igrid,midg 7.2631347E-03 1.7263316E-02 1,midg,midg; igrid,midg,midg -1.7820247E-02 -8.9810472E-03 gauss-seidel spectral radius is 0.9982954 estimated iterations to convergence 192 setup time was (sec) 0.7900000 now iterating at: 17:15:48 rms-change max change #iterations 3.722500 172.7330 at 10iterations 1.588542 60.95598 at 20iterations 0.6813172 23.94527 at 30iterations 0.2922479 11.16994 at 40iterations 0.1256183 4.580143 at 50iterations 5.3727079E-02 1.775841 at 60iterations 2.3148267E-02 0.8106351 at 70iterations 9.9155372E-03 0.3447876 at 80iterations 4.2806184E-03 0.1456318 at 90iterations 1.8467875E-03 5.8169365E-02 at 100iterations 7.9853676E-04 2.5629044E-02 at 110iterations 3.5184243E-04 1.2154579E-02 at 120iterations finished qdiffx linear iterations at : 17:15:54 total time elapsed so far: 6.880000 # loops : 120 mean,max change (kT/e) : 3.5184243E-04 1.2154579E-02 energy calculations done at 6.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.070000 DelPhi exited at 17:15:55 7.069u 0.167s 0:07.66 94.2% 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 Sat Oct 8 2011 at 17:15:55 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 = 3366 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.496883 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): 37.17600 95.02299 ymin,ymax (A): 16.70400 80.86400 zmin,zma (A): -22.67200 26.68000 x,y,z range (A): 57.84699 64.16000 49.35200 scale (grids/A): 2.496883 object centre (A): 66.09950 48.78400 2.004001 number of atom coordinates read : 3366 total number of charged atoms : 3220 net assigned charge : -6.499982 assigned positive charge : 503.9186 centred at (gu) : 89.61262 90.38693 88.26469 assigned negative charge : -510.4198 centred at (gu) : 89.67964 90.28632 88.16119 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 174820 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29082 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 84860 mr = 127762 m= 26096 mr = 68356 m= 4846 mr = 20142 m= 430 mr = 3272 m= 10 mr = 240 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 71290 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 25742 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) : 1.664589 object centre at (A) : 66.09950 48.78400 2.004001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.8890424E-02 -5.0049756E-02 midg,1,midg; midg,igrid,midg 0.2622708 0.5351199 1,midg,midg; igrid,midg,midg -0.2758498 -0.1013768 gauss-seidel spectral radius is 0.9991806 estimated iterations to convergence 276 setup time was (sec) 1.550000 now iterating at: 17:15:57 rms-change max change #iterations 9.500306 255.9761 at 10iterations 5.411634 115.5703 at 20iterations 3.060303 61.34724 at 30iterations 1.723353 32.72782 at 40iterations 0.9701486 18.65872 at 50iterations 0.5451773 10.57859 at 60iterations 0.3053670 6.267132 at 70iterations 0.1706539 3.330540 at 80iterations 9.5680870E-02 1.957746 at 90iterations 5.3443179E-02 1.141262 at 100iterations 2.9851984E-02 0.5946655 at 110iterations 1.6710628E-02 0.3104995 at 120iterations 9.3321800E-03 0.1698086 at 130iterations 5.2090618E-03 0.1085715 at 140iterations 2.9169570E-03 5.6033134E-02 at 150iterations 1.6360253E-03 3.0322075E-02 at 160iterations 9.2237926E-04 1.8704414E-02 at 170iterations 5.2320765E-04 9.7322464E-03 at 180iterations finished qdiffx linear iterations at : 17:16:06 total time elapsed so far: 11.24000 # loops : 180 mean,max change (kT/e) : 5.2320765E-04 9.7322464E-03 energy calculations done at 11.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.42000 DelPhi exited at 17:16:07 11.427u 0.207s 0:11.94 97.3% 0+0k 0+0io 0pf+0w