Tue Oct 11 06:42:22 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 Tue Oct 11 2011 at 06:42:22 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 = 1594 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: 0.7356740 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): 36.93200 81.27200 ymin,ymax (A): 6.737999 42.05500 zmin,zma (A): -12.03400 36.35700 x,y,z range (A): 44.33999 35.31700 48.39100 scale (grids/A): 0.7356740 object centre (A): 59.10200 24.39650 12.16150 number of atom coordinates read : 1594 total number of charged atoms : 1541 net assigned charge : 7.000008 assigned positive charge : 246.6356 centred at (gu) : 88.83196 89.47688 90.04043 assigned negative charge : -239.6354 centred at (gu) : 88.81348 89.37141 90.03574 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6088 nv = 96 ne = 84 npr = 29965 no. pairs analyzed = 29965 no. exposed pairs = 2161 no. arc points = 15140 no. surface atoms = 728 nbur = 866 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 395 mr = 3227 m= 2 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 7.9999983E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3187 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1394 ## 116 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6549 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0873403E-07 1.1689583E-07 midg,1,midg; midg,igrid,midg 4.2080764E-08 1.6824121E-07 1,midg,midg; igrid,midg,midg 1.2342015E-07 1.0166585E-07 gauss-seidel spectral radius is 0.9903216 estimated iterations to convergence 83 setup time was (sec) 0.4800000 now iterating at: 06:42:22 rms-change max change #iterations 0.2003450 27.65579 at 10iterations 2.6635513E-02 4.288895 at 20iterations 3.4685638E-03 0.5246897 at 30iterations 4.6074818E-04 7.0838928E-02 at 40iterations 6.1303443E-05 8.4609985E-03 at 50iterations finished qdiffx linear iterations at : 06:42:25 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 6.1303443E-05 8.4609985E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 06:42:26 3.438u 0.181s 0:04.03 89.5% 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 Tue Oct 11 2011 at 06:42:26 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 = 1594 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.207022 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): 36.93200 81.27200 ymin,ymax (A): 6.737999 42.05500 zmin,zma (A): -12.03400 36.35700 x,y,z range (A): 44.33999 35.31700 48.39100 scale (grids/A): 2.207022 object centre (A): 59.10200 24.39650 12.16150 number of atom coordinates read : 1594 total number of charged atoms : 1541 net assigned charge : 7.000008 assigned positive charge : 246.6356 centred at (gu) : 86.49619 88.43099 90.12174 assigned negative charge : -239.6354 centred at (gu) : 86.44064 88.11446 90.10757 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 63897 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15140 grid for indexing accessible points = 1.400000 m= 25583 mr = 43446 m= 5179 mr = 18961 m= 512 mr = 3256 m= 12 mr = 213 m= 0 mr = 6 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 29301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 42 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 12263 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) : 0.7356740 object centre at (A) : 59.10200 24.39650 12.16150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1822668E-02 4.6746675E-02 midg,1,midg; midg,igrid,midg -4.0729009E-03 3.2082271E-02 1,midg,midg; igrid,midg,midg 4.5266345E-02 3.0521516E-02 gauss-seidel spectral radius is 0.9988709 estimated iterations to convergence 236 setup time was (sec) 0.8200000 now iterating at: 06:42:27 rms-change max change #iterations 4.236883 186.8841 at 10iterations 2.114897 80.78448 at 20iterations 1.062952 36.43399 at 30iterations 0.5338306 21.07615 at 40iterations 0.2672318 9.384988 at 50iterations 0.1337380 4.463034 at 60iterations 6.6770785E-02 2.070163 at 70iterations 3.3545762E-02 1.015999 at 80iterations 1.6806642E-02 0.6242676 at 90iterations 8.4444135E-03 0.2675018 at 100iterations 4.2187450E-03 0.1400781 at 110iterations 2.1161560E-03 6.3171387E-02 at 120iterations finished qdiffx linear iterations at : 06:42:34 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 2.1161560E-03 6.3171387E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 06:42:35 7.827u 0.218s 0:09.05 88.7% 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 Tue Oct 11 2011 at 06:42:35 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 = 1594 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.310533 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): 36.93200 81.27200 ymin,ymax (A): 6.737999 42.05500 zmin,zma (A): -12.03400 36.35700 x,y,z range (A): 44.33999 35.31700 48.39100 scale (grids/A): 3.310533 object centre (A): 59.10200 24.39650 12.16150 number of atom coordinates read : 1594 total number of charged atoms : 1541 net assigned charge : 7.000008 assigned positive charge : 246.6356 centred at (gu) : 84.74445 87.64648 90.18279 assigned negative charge : -239.6354 centred at (gu) : 84.66119 87.17180 90.16148 start vw surface at 0.1400000 fill in re-entrant regions at 0.7400000 boundary points on vw surface= 146841 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15140 grid for indexing accessible points = 1.400000 m= 78701 mr = 104904 m= 32998 mr = 64404 m= 9800 mr = 26481 m= 1911 mr = 7223 m= 224 mr = 1295 m= 12 mr = 134 m= 0 mr = 4 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.650000 number of dielectric boundary points 66042 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 12328 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) : 2.207022 object centre at (A) : 59.10200 24.39650 12.16150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2580926 0.4097179 midg,1,midg; midg,igrid,midg -6.4314738E-02 0.2454783 1,midg,midg; igrid,midg,midg 0.5739790 0.2645173 gauss-seidel spectral radius is 0.9993071 estimated iterations to convergence 300 setup time was (sec) 1.960000 now iterating at: 06:42:37 rms-change max change #iterations 9.368987 271.8333 at 10iterations 5.591506 119.3794 at 20iterations 3.317898 65.51540 at 30iterations 1.961933 39.34819 at 40iterations 1.158710 25.89473 at 50iterations 0.6843703 13.27814 at 60iterations 0.4010648 7.264448 at 70iterations 0.2359355 4.735312 at 80iterations 0.1389988 2.885436 at 90iterations 8.1634939E-02 1.688482 at 100iterations 4.7815949E-02 0.8653450 at 110iterations 2.8078850E-02 0.5655193 at 120iterations 1.6503667E-02 0.3162003 at 130iterations 9.6812919E-03 0.1799457 at 140iterations 5.6884792E-03 0.1032104 at 150iterations 3.3678918E-03 6.3537598E-02 at 160iterations 1.9949325E-03 4.1110992E-02 at 170iterations 1.1996732E-03 2.3035049E-02 at 180iterations finished qdiffx linear iterations at : 06:42:48 total time elapsed so far: 12.84000 # loops : 180 mean,max change (kT/e) : 1.1996732E-03 2.3035049E-02 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.06000 DelPhi exited at 06:42:50 13.064u 0.227s 0:15.29 86.8% 0+0k 0+0io 0pf+0w