Wed Feb 15 08:59:30 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:59:30 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 = 4320 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5849395 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): -25.70200 35.15900 ymin,ymax (A): 38.08600 98.66600 zmin,zma (A): 31.02100 90.57800 x,y,z range (A): 60.86100 60.58000 59.55699 scale (grids/A): 0.5849395 object centre (A): 4.728498 68.37600 60.79950 number of atom coordinates read : 4320 total number of charged atoms : 4161 net assigned charge : -1.999960 assigned positive charge : 646.9775 centred at (gu) : 90.70900 87.79436 88.70947 assigned negative charge : -648.9806 centred at (gu) : 90.59572 87.93005 88.85958 start vw surface at 0.1700000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 9612 nv = 96 ne = 84 npr = 90417 no. pairs analyzed = 90417 no. exposed pairs = 4939 no. arc points = 33703 no. surface atoms = 1681 nbur = 2639 mkacc time = 0.2300000 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 = 1.484000 m= 461 mr = 5597 m= 4 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 82 time to turn everything in is 0.5000000 number of dielectric boundary points 4428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3586 ## 407 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 12548 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.5282957E-09 -4.7932671E-09 midg,1,midg; midg,igrid,midg 7.2645849E-09 -3.5455519E-09 1,midg,midg; igrid,midg,midg -4.2816377E-09 4.0896828E-09 gauss-seidel spectral radius is 0.9850117 estimated iterations to convergence 67 setup time was (sec) 0.8200000 now iterating at: 08:59:32 rms-change max change #iterations 0.1270763 18.93219 at 10iterations 1.0515321E-02 1.620346 at 20iterations 1.2215698E-03 0.1647034 at 30iterations 2.7547538E-04 3.7544250E-02 at 40iterations 9.2014052E-05 1.0582685E-02 at 50iterations finished qdiffx linear iterations at : 08:59:37 total time elapsed so far: 5.730000 # loops : 50 mean,max change (kT/e) : 9.2014052E-05 1.0582685E-02 energy calculations done at 5.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.900000 DelPhi exited at 08:59:37 5.906u 0.439s 0:06.67 94.9% 0+0k 0+0io 6pf+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 Wed Feb 15 2012 at 08:59:37 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 = 4320 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.754818 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): -25.70200 35.15900 ymin,ymax (A): 38.08600 98.66600 zmin,zma (A): 31.02100 90.57800 x,y,z range (A): 60.86100 60.58000 59.55699 scale (grids/A): 1.754818 object centre (A): 4.728498 68.37600 60.79950 number of atom coordinates read : 4320 total number of charged atoms : 4161 net assigned charge : -1.999960 assigned positive charge : 646.9775 centred at (gu) : 92.12585 83.38202 86.12709 assigned negative charge : -648.9806 centred at (gu) : 91.78657 83.78970 86.57822 start vw surface at 0.1600000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 106611 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33703 grid for indexing accessible points = 1.400000 m= 37496 mr = 77328 m= 5084 mr = 27918 m= 193 mr = 3079 m= 0 mr = 53 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 4674 time to turn everything in is 0.8900000 number of dielectric boundary points 41006 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 339 ## 2 charges are in solution ## iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 32374 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) : 0.5849395 object centre at (A) : 4.728498 68.37600 60.79950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7927787E-02 -3.1448275E-02 midg,1,midg; midg,igrid,midg 4.5317847E-02 -8.3667021E-03 1,midg,midg; igrid,midg,midg -1.7064184E-02 3.8292889E-02 gauss-seidel spectral radius is 0.9985477 estimated iterations to convergence 208 setup time was (sec) 1.270000 now iterating at: 08:59:39 rms-change max change #iterations 4.834129 158.8812 at 10iterations 2.200993 67.00580 at 20iterations 1.004685 28.15867 at 30iterations 0.4610641 12.95087 at 40iterations 0.2124196 5.884407 at 50iterations 9.6731335E-02 2.697517 at 60iterations 4.4567738E-02 1.385163 at 70iterations 2.0443758E-02 0.6015644 at 80iterations 9.4091473E-03 0.2615101 at 90iterations 4.3471195E-03 0.1356926 at 100iterations 2.0346208E-03 5.6388855E-02 at 110iterations 9.7149209E-04 2.5237083E-02 at 120iterations finished qdiffx linear iterations at : 08:59:52 total time elapsed so far: 14.39000 # loops : 120 mean,max change (kT/e) : 9.7149209E-04 2.5237083E-02 energy calculations done at 14.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.57000 DelPhi exited at 08:59:53 14.578u 0.524s 0:15.41 97.9% 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 Wed Feb 15 2012 at 08:59:53 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 = 4320 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.632228 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): -25.70200 35.15900 ymin,ymax (A): 38.08600 98.66600 zmin,zma (A): 31.02100 90.57800 x,y,z range (A): 60.86100 60.58000 59.55699 scale (grids/A): 2.632228 object centre (A): 4.728498 68.37600 60.79950 number of atom coordinates read : 4320 total number of charged atoms : 4161 net assigned charge : -1.999960 assigned positive charge : 646.9775 centred at (gu) : 93.18858 80.07277 84.19038 assigned negative charge : -648.9806 centred at (gu) : 92.67989 80.68428 84.86745 start vw surface at 0.1700000 fill in re-entrant regions at 0.7400000 boundary points on vw surface= 247181 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33703 grid for indexing accessible points = 1.400000 m= 125509 mr = 187249 m= 41323 mr = 103823 m= 8900 mr = 33158 m= 1016 mr = 6712 m= 26 mr = 599 m= 0 mr = 4 time to grow re-entrant surface = 1.430000 no. cavity mid-points inaccessible to solvent = 15815 time to turn everything in is 2.330000 number of dielectric boundary points 92410 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 2.520000 number of grid points assigned charge 33280 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) : 1.754818 object centre at (A) : 4.728498 68.37600 60.79950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9844975 -0.3541543 midg,1,midg; midg,igrid,midg 0.6051257 -9.4671562E-02 1,midg,midg; igrid,midg,midg -0.3187399 0.5293138 gauss-seidel spectral radius is 0.9992626 estimated iterations to convergence 291 setup time was (sec) 2.760000 now iterating at: 08:59:56 rms-change max change #iterations 11.72211 338.1187 at 10iterations 6.878346 141.8282 at 20iterations 4.007469 71.68608 at 30iterations 2.326819 41.37225 at 40iterations 1.353124 22.17662 at 50iterations 0.7827181 13.99241 at 60iterations 0.4520295 7.153226 at 70iterations 0.2616523 4.199262 at 80iterations 0.1510998 2.396964 at 90iterations 8.7273955E-02 1.388108 at 100iterations 5.0351053E-02 0.8208265 at 110iterations 2.9106565E-02 0.5270252 at 120iterations 1.6814981E-02 0.2628279 at 130iterations 9.7684721E-03 0.1496582 at 140iterations 5.7121003E-03 8.9908600E-02 at 150iterations 3.3835119E-03 5.1709652E-02 at 160iterations 2.0459355E-03 3.1811714E-02 at 170iterations 1.2749961E-03 2.0477295E-02 at 180iterations finished qdiffx linear iterations at : 09:00:18 total time elapsed so far: 24.99000 # loops : 180 mean,max change (kT/e) : 1.2749961E-03 2.0477295E-02 energy calculations done at 24.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 25.17000 DelPhi exited at 09:00:19 25.170u 0.566s 0:26.08 98.6% 0+0k 0+0io 0pf+0w