Sat Oct 8 17:59:16 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+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 17:59:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3354 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: 0.5379757 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): -49.93500 5.245000 ymin,ymax (A): -125.8480 -59.67400 zmin,zma (A): -16.54300 29.33200 x,y,z range (A): 55.18000 66.17400 45.87500 scale (grids/A): 0.5379757 object centre (A): -22.34500 -92.76100 6.394501 number of atom coordinates read : 3354 total number of charged atoms : 3208 net assigned charge : -4.999993 assigned positive charge : 503.2576 centred at (gu) : 90.17570 90.51216 89.94378 assigned negative charge : -508.2589 centred at (gu) : 90.10392 90.58304 89.94124 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6314 nv = 96 ne = 84 npr = 67449 no. pairs analyzed = 67449 no. exposed pairs = 4253 no. arc points = 29392 no. surface atoms = 1443 nbur = 1911 mkacc time = 0.1600000 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= 250 mr = 3326 m= 0 mr = 7 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3231 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2967 ## 404 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8303 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4244165E-10 -2.0779532E-10 midg,1,midg; midg,igrid,midg 1.4732508E-10 -7.1237621E-10 1,midg,midg; igrid,midg,midg -6.0410216E-10 1.8266882E-10 gauss-seidel spectral radius is 0.9822198 estimated iterations to convergence 62 setup time was (sec) 0.6200000 now iterating at: 17:59:17 rms-change max change #iterations 7.3694654E-02 12.48102 at 10iterations 4.7865408E-03 0.7536497 at 20iterations 4.9823400E-04 8.8484764E-02 at 30iterations 1.1698209E-04 2.5589943E-02 at 40iterations 3.4749450E-05 7.7195168E-03 at 50iterations finished qdiffx linear iterations at : 17:59:21 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 3.4749450E-05 7.7195168E-03 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 17:59:21 4.256u 0.237s 0:04.79 93.5% 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 Sat Oct 8 2011 at 17:59:21 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3354 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: 1.613927 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): -49.93500 5.245000 ymin,ymax (A): -125.8480 -59.67400 zmin,zma (A): -16.54300 29.33200 x,y,z range (A): 55.18000 66.17400 45.87500 scale (grids/A): 1.613927 object centre (A): -22.34500 -92.76100 6.394501 number of atom coordinates read : 3354 total number of charged atoms : 3208 net assigned charge : -4.999993 assigned positive charge : 503.2576 centred at (gu) : 90.52598 91.53572 89.83067 assigned negative charge : -508.2589 centred at (gu) : 90.31170 91.74841 89.82346 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 70623 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29392 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 22191 mr = 48688 m= 2251 mr = 15377 m= 63 mr = 1052 m= 0 mr = 2 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 513 time to turn everything in is 0.5300000 number of dielectric boundary points 30009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 367 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 24574 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) : 0.5379757 object centre at (A) : -22.34500 -92.76100 6.394501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4654453E-03 -1.6298532E-03 midg,1,midg; midg,igrid,midg 1.3648153E-02 -4.0443720E-05 1,midg,midg; igrid,midg,midg -8.0896951E-03 3.1684309E-03 gauss-seidel spectral radius is 0.9981782 estimated iterations to convergence 186 setup time was (sec) 0.8500000 now iterating at: 17:59:22 rms-change max change #iterations 3.457400 172.5250 at 10iterations 1.436896 58.31389 at 20iterations 0.5971214 19.37309 at 30iterations 0.2485476 8.827408 at 40iterations 0.1036234 3.904518 at 50iterations 4.3213006E-02 1.556624 at 60iterations 1.8063391E-02 0.6641407 at 70iterations 7.5643212E-03 0.2524796 at 80iterations 3.1788500E-03 0.1088893 at 90iterations 1.3520774E-03 5.0107956E-02 at 100iterations 5.9490767E-04 2.4389267E-02 at 110iterations 2.7603935E-04 1.0435104E-02 at 120iterations finished qdiffx linear iterations at : 17:59:31 total time elapsed so far: 9.380000 # loops : 120 mean,max change (kT/e) : 2.7603935E-04 1.0435104E-02 energy calculations done at 9.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.550000 DelPhi exited at 17:59:31 9.557u 0.296s 0:10.15 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 Sat Oct 8 2011 at 17:59:31 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 = 3354 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: 2.420891 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): -49.93500 5.245000 ymin,ymax (A): -125.8480 -59.67400 zmin,zma (A): -16.54300 29.33200 x,y,z range (A): 55.18000 66.17400 45.87500 scale (grids/A): 2.420891 object centre (A): -22.34500 -92.76100 6.394501 number of atom coordinates read : 3354 total number of charged atoms : 3208 net assigned charge : -4.999993 assigned positive charge : 503.2576 centred at (gu) : 90.78889 92.30314 89.74570 assigned negative charge : -508.2589 centred at (gu) : 90.46735 92.62255 89.73505 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 164030 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29392 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 77588 mr = 119219 m= 21747 mr = 61608 m= 3356 mr = 16257 m= 255 mr = 2142 m= 7 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 1665 time to turn everything in is 1.320000 number of dielectric boundary points 67654 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 25624 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) : 1.613927 object centre at (A) : -22.34500 -92.76100 6.394501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1008200 -2.0278068E-02 midg,1,midg; midg,igrid,midg 0.3802725 0.2538733 1,midg,midg; igrid,midg,midg -0.1108799 7.2886005E-02 gauss-seidel spectral radius is 0.9991426 estimated iterations to convergence 270 setup time was (sec) 1.660000 now iterating at: 17:59:33 rms-change max change #iterations 9.059959 348.8173 at 10iterations 5.091175 144.2654 at 20iterations 2.850144 63.17377 at 30iterations 1.583058 35.05267 at 40iterations 0.8817378 17.90297 at 50iterations 0.4898889 9.853184 at 60iterations 0.2707560 5.681381 at 70iterations 0.1498594 2.765967 at 80iterations 8.2646899E-02 1.703744 at 90iterations 4.5708753E-02 0.8841628 at 100iterations 2.5189182E-02 0.4980507 at 110iterations 1.3906959E-02 0.2654974 at 120iterations 7.6714419E-03 0.1488495 at 130iterations 4.2351200E-03 8.1596375E-02 at 140iterations 2.3438346E-03 4.4790268E-02 at 150iterations 1.2976613E-03 2.7145386E-02 at 160iterations 7.2643784E-04 1.4766693E-02 at 170iterations 4.1132569E-04 8.4710717E-03 at 180iterations finished qdiffx linear iterations at : 17:59:47 total time elapsed so far: 15.31000 # loops : 180 mean,max change (kT/e) : 4.1132569E-04 8.4710717E-03 energy calculations done at 15.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.50000 DelPhi exited at 17:59:47 15.500u 0.266s 0:16.10 97.8% 0+0k 0+0io 0pf+0w