Sun Oct 9 15:25:36 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 15:25:36 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5192 !!! WARNING: GLM 509 has a net charge of -0.0940 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: 0.4992008 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): 8.327001 63.77400 ymin,ymax (A): 53.51000 124.8240 zmin,zma (A): 32.26600 96.53900 x,y,z range (A): 55.44700 71.31400 64.27300 scale (grids/A): 0.4992008 object centre (A): 36.05050 89.16700 64.40250 number of atom coordinates read : 5192 total number of charged atoms : 5025 net assigned charge : 3.906030 assigned positive charge : 806.9641 centred at (gu) : 89.25230 90.24418 90.23670 assigned negative charge : -803.0646 centred at (gu) : 89.29007 90.18051 90.09882 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7828 nv = 96 ne = 84 npr = 105156 no. pairs analyzed = 105156 no. exposed pairs = 6387 no. arc points = 44089 no. surface atoms = 2143 nbur = 3049 mkacc time = 0.1800000 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 = 1.708000 m= 254 mr = 4065 m= 0 mr = 8 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3400000 number of dielectric boundary points 4009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4289 ## 733 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 10830 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0377203E-10 2.8957212E-10 midg,1,midg; midg,igrid,midg -7.6837071E-11 1.5332621E-10 1,midg,midg; igrid,midg,midg 1.2024777E-10 -2.8867931E-11 gauss-seidel spectral radius is 0.9795008 estimated iterations to convergence 58 setup time was (sec) 0.5200000 now iterating at: 15:25:37 rms-change max change #iterations 6.2581390E-02 11.38808 at 10iterations 3.7247005E-03 0.5925663 at 20iterations 6.1232160E-04 7.9129219E-02 at 30iterations 2.0648782E-04 3.2120705E-02 at 40iterations 7.3191557E-05 1.2626171E-02 at 50iterations finished qdiffx linear iterations at : 15:25:40 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 7.3191557E-05 1.2626171E-02 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 15:25:40 3.558u 0.192s 0:04.10 91.2% 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 Sun Oct 9 2011 at 15:25:40 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5192 !!! WARNING: GLM 509 has a net charge of -0.0940 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: 1.497602 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): 8.327001 63.77400 ymin,ymax (A): 53.51000 124.8240 zmin,zma (A): 32.26600 96.53900 x,y,z range (A): 55.44700 71.31400 64.27300 scale (grids/A): 1.497602 object centre (A): 36.05050 89.16700 64.40250 number of atom coordinates read : 5192 total number of charged atoms : 5025 net assigned charge : 3.906030 assigned positive charge : 806.9641 centred at (gu) : 87.75535 90.73104 90.70838 assigned negative charge : -803.0646 centred at (gu) : 87.86965 90.54129 90.29633 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 89289 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44089 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 24915 mr = 61176 m= 1880 mr = 16411 m= 34 mr = 798 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1909 time to turn everything in is 0.4300000 number of dielectric boundary points 37733 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 703 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 37460 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) : 0.4992008 object centre at (A) : 36.05050 89.16700 64.40250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0284434E-03 1.4088347E-02 midg,1,midg; midg,igrid,midg -5.6535881E-03 1.5574764E-02 1,midg,midg; igrid,midg,midg 3.0467031E-03 5.9963221E-04 gauss-seidel spectral radius is 0.9980417 estimated iterations to convergence 180 setup time was (sec) 0.6600000 now iterating at: 15:25:41 rms-change max change #iterations 3.835235 147.0996 at 10iterations 1.543717 54.96360 at 20iterations 0.6227615 21.28458 at 30iterations 0.2500265 8.093704 at 40iterations 0.1011816 3.257751 at 50iterations 4.1065931E-02 1.604538 at 60iterations 1.6611176E-02 0.5231802 at 70iterations 6.7686085E-03 0.2612877 at 80iterations 2.7867558E-03 9.9817276E-02 at 90iterations 1.1857477E-03 3.4133315E-02 at 100iterations 5.3837663E-04 1.7918587E-02 at 110iterations 2.7446728E-04 9.8171234E-03 at 120iterations finished qdiffx linear iterations at : 15:25:48 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 2.7446728E-04 9.8171234E-03 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 15:25:49 7.973u 0.205s 0:08.44 96.8% 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 Sun Oct 9 2011 at 15:25:49 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5192 !!! WARNING: GLM 509 has a net charge of -0.0940 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: 2.246403 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): 8.327001 63.77400 ymin,ymax (A): 53.51000 124.8240 zmin,zma (A): 32.26600 96.53900 x,y,z range (A): 55.44700 71.31400 64.27300 scale (grids/A): 2.246403 object centre (A): 36.05050 89.16700 64.40250 number of atom coordinates read : 5192 total number of charged atoms : 5025 net assigned charge : 3.906030 assigned positive charge : 806.9641 centred at (gu) : 86.63268 91.09630 91.06231 assigned negative charge : -803.0646 centred at (gu) : 86.80437 90.81180 90.44419 start vw surface at 0.1400000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 208782 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44089 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 90173 mr = 150995 m= 21574 mr = 69938 m= 2658 mr = 15513 m= 101 mr = 1580 m= 0 mr = 20 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 6562 time to turn everything in is 1.070000 number of dielectric boundary points 85242 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 40063 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) : 1.497602 object centre at (A) : 36.05050 89.16700 64.40250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.6500429E-02 0.2421648 midg,1,midg; midg,igrid,midg -0.2128233 0.2090627 1,midg,midg; igrid,midg,midg 6.0871799E-02 2.4890961E-02 gauss-seidel spectral radius is 0.9991460 estimated iterations to convergence 270 setup time was (sec) 1.310000 now iterating at: 15:25:50 rms-change max change #iterations 10.55519 300.9913 at 10iterations 5.991146 160.7534 at 20iterations 3.390052 74.74135 at 30iterations 1.905344 46.21133 at 40iterations 1.068364 23.52909 at 50iterations 0.5959272 12.87563 at 60iterations 0.3318525 6.398396 at 70iterations 0.1848486 3.575855 at 80iterations 0.1024204 2.093960 at 90iterations 5.6749020E-02 1.053528 at 100iterations 3.1421583E-02 0.5953903 at 110iterations 1.7424585E-02 0.3929749 at 120iterations 9.6240519E-03 0.2044735 at 130iterations 5.3206962E-03 0.1034307 at 140iterations 2.9400887E-03 7.0373535E-02 at 150iterations 1.6300182E-03 3.0658722E-02 at 160iterations 8.9749205E-04 1.7021179E-02 at 170iterations 4.9708516E-04 9.3078613E-03 at 180iterations finished qdiffx linear iterations at : 15:26:02 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 4.9708516E-04 9.3078613E-03 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 15:26:02 13.081u 0.204s 0:13.54 98.0% 0+0k 0+0io 0pf+0w