Mon Oct 10 09:19:08 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 Mon Oct 10 2011 at 09:19:08 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 = 2915 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: 0.5803055 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): -17.82800 33.85600 ymin,ymax (A): -58.79200 -1.199000 zmin,zma (A): -1.368000 59.97900 x,y,z range (A): 51.68400 57.59300 61.34700 scale (grids/A): 0.5803055 object centre (A): 8.013999 -29.99550 29.30550 number of atom coordinates read : 2915 total number of charged atoms : 2763 net assigned charge : 8.000022 assigned positive charge : 423.9498 centred at (gu) : 88.92495 87.96119 87.62566 assigned negative charge : -415.9503 centred at (gu) : 88.99180 87.78687 87.52516 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6639 nv = 96 ne = 84 npr = 56537 no. pairs analyzed = 56537 no. exposed pairs = 4362 no. arc points = 32632 no. surface atoms = 1444 nbur = 1471 mkacc time = 9.0000004E-02 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= 355 mr = 2862 m= 3 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 4120 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3124 ## 342 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8350 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7194371E-10 2.2638365E-09 midg,1,midg; midg,igrid,midg -2.9821483E-09 3.3500398E-09 1,midg,midg; igrid,midg,midg 4.1488670E-09 3.9537365E-10 gauss-seidel spectral radius is 0.9846887 estimated iterations to convergence 66 setup time was (sec) 0.4000000 now iterating at: 09:19:09 rms-change max change #iterations 9.6240230E-02 18.55006 at 10iterations 7.2026355E-03 1.141445 at 20iterations 5.7387719E-04 8.8645935E-02 at 30iterations 5.3121839E-05 7.9026222E-03 at 40iterations 7.7698251E-06 9.0789795E-04 at 50iterations finished qdiffx linear iterations at : 09:19:12 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 7.7698251E-06 9.0789795E-04 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 09:19:12 3.415u 0.171s 0:03.85 92.9% 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 Mon Oct 10 2011 at 09:19:12 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 = 2915 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: 1.740916 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): -17.82800 33.85600 ymin,ymax (A): -58.79200 -1.199000 zmin,zma (A): -1.368000 59.97900 x,y,z range (A): 51.68400 57.59300 61.34700 scale (grids/A): 1.740916 object centre (A): 8.013999 -29.99550 29.30550 number of atom coordinates read : 2915 total number of charged atoms : 2763 net assigned charge : 8.000022 assigned positive charge : 423.9498 centred at (gu) : 86.77432 83.88322 82.87675 assigned negative charge : -415.9503 centred at (gu) : 86.97501 83.36044 82.57516 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70963 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32632 grid for indexing accessible points = 1.400000 m= 22148 mr = 42840 m= 2975 mr = 14003 m= 136 mr = 1308 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 38058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 271 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 21464 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) : 0.5803055 object centre at (A) : 8.013999 -29.99550 29.30550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.4052298E-03 4.6858625E-03 midg,1,midg; midg,igrid,midg 8.4575498E-03 2.9685397E-02 1,midg,midg; igrid,midg,midg 1.0922386E-02 1.4387689E-02 gauss-seidel spectral radius is 0.9984282 estimated iterations to convergence 200 setup time was (sec) 0.5700000 now iterating at: 09:19:13 rms-change max change #iterations 3.699495 188.1983 at 10iterations 1.631763 55.62861 at 20iterations 0.7203586 26.51609 at 30iterations 0.3190647 10.60541 at 40iterations 0.1408469 4.638092 at 50iterations 6.2491462E-02 2.236284 at 60iterations 2.7530687E-02 0.9424791 at 70iterations 1.2234381E-02 0.4419212 at 80iterations 5.4098754E-03 0.2068348 at 90iterations 2.3877253E-03 8.4372520E-02 at 100iterations 1.0557896E-03 3.8204193E-02 at 110iterations 4.6621071E-04 1.4553070E-02 at 120iterations finished qdiffx linear iterations at : 09:19:20 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 4.6621071E-04 1.4553070E-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) 7.780000 DelPhi exited at 09:19:21 7.786u 0.194s 0:08.27 96.3% 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 Mon Oct 10 2011 at 09:19:21 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 = 2915 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: 2.611375 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): -17.82800 33.85600 ymin,ymax (A): -58.79200 -1.199000 zmin,zma (A): -1.368000 59.97900 x,y,z range (A): 51.68400 57.59300 61.34700 scale (grids/A): 2.611375 object centre (A): 8.013999 -29.99550 29.30550 number of atom coordinates read : 2915 total number of charged atoms : 2763 net assigned charge : 8.000022 assigned positive charge : 423.9498 centred at (gu) : 85.16128 80.82477 79.31501 assigned negative charge : -415.9503 centred at (gu) : 85.46246 80.04057 78.86262 start vw surface at 0.1100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 163566 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32632 grid for indexing accessible points = 1.400000 m= 72575 mr = 105658 m= 23934 mr = 53877 m= 4758 mr = 16899 m= 513 mr = 2851 m= 15 mr = 203 m= 0 mr = 4 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9100000 number of dielectric boundary points 85869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 22090 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) : 1.740916 object centre at (A) : 8.013999 -29.99550 29.30550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3783527E-02 4.6110749E-02 midg,1,midg; midg,igrid,midg 0.2019797 0.3570766 1,midg,midg; igrid,midg,midg 4.4167679E-02 0.1765146 gauss-seidel spectral radius is 0.9992341 estimated iterations to convergence 285 setup time was (sec) 1.160000 now iterating at: 09:19:22 rms-change max change #iterations 9.482786 387.2455 at 10iterations 5.678754 171.4905 at 20iterations 3.342003 87.92180 at 30iterations 1.948933 57.87086 at 40iterations 1.128463 29.76242 at 50iterations 0.6512558 18.29163 at 60iterations 0.3752545 8.688548 at 70iterations 0.2159089 4.597256 at 80iterations 0.1237847 2.909054 at 90iterations 7.1024306E-02 1.566162 at 100iterations 4.0504016E-02 0.9292068 at 110iterations 2.3139035E-02 0.5317574 at 120iterations 1.3182114E-02 0.2842216 at 130iterations 7.5287437E-03 0.1542654 at 140iterations 4.2922297E-03 9.9193215E-02 at 150iterations 2.4417858E-03 5.2104950E-02 at 160iterations 1.3903845E-03 2.8889179E-02 at 170iterations 7.9241517E-04 1.5441895E-02 at 180iterations finished qdiffx linear iterations at : 09:19:34 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 7.9241517E-04 1.5441895E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 09:19:34 12.888u 0.193s 0:13.34 97.9% 0+0k 0+0io 0pf+0w