Tue Oct 11 04:00:07 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 Tue Oct 11 2011 at 04:00:07 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 !!! WARNING: ARG 217 has a net charge of 1.2720 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6353512 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): -11.62600 36.90700 ymin,ymax (A): -25.80700 22.47300 zmin,zma (A): -10.61400 45.41800 x,y,z range (A): 48.53300 48.28000 56.03201 scale (grids/A): 0.6353512 object centre (A): 12.64050 -1.667000 17.40200 number of atom coordinates read : 2726 total number of charged atoms : 2574 net assigned charge : 1.412011 assigned positive charge : 413.3188 centred at (gu) : 90.25410 90.19100 91.95576 assigned negative charge : -411.9073 centred at (gu) : 90.01167 90.03228 91.89143 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7231 nv = 96 ne = 84 npr = 56060 no. pairs analyzed = 56060 no. exposed pairs = 3274 no. arc points = 22908 no. surface atoms = 1099 nbur = 1627 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 412 mr = 4080 m= 0 mr = 49 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 3514 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2298 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8846 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5412195E-09 1.3085668E-08 midg,1,midg; midg,igrid,midg -1.5300934E-08 1.9304043E-08 1,midg,midg; igrid,midg,midg -2.4071761E-08 2.8768497E-08 gauss-seidel spectral radius is 0.9871734 estimated iterations to convergence 72 setup time was (sec) 0.6200000 now iterating at: 04:00:08 rms-change max change #iterations 0.1489247 26.13741 at 10iterations 1.4751987E-02 1.987759 at 20iterations 1.5145700E-03 0.2247334 at 30iterations 1.6441828E-04 2.3882687E-02 at 40iterations 2.3512526E-05 3.5400391E-03 at 50iterations finished qdiffx linear iterations at : 04:00:11 total time elapsed so far: 3.800000 # loops : 50 mean,max change (kT/e) : 2.3512526E-05 3.5400391E-03 energy calculations done at 3.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.980000 DelPhi exited at 04:00:12 3.982u 0.247s 0:04.69 89.9% 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 Tue Oct 11 2011 at 04:00:12 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 !!! WARNING: ARG 217 has a net charge of 1.2720 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.906054 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): -11.62600 36.90700 ymin,ymax (A): -25.80700 22.47300 zmin,zma (A): -10.61400 45.41800 x,y,z range (A): 48.53300 48.28000 56.03201 scale (grids/A): 1.906054 object centre (A): 12.64050 -1.667000 17.40200 number of atom coordinates read : 2726 total number of charged atoms : 2574 net assigned charge : 1.412011 assigned positive charge : 413.3188 centred at (gu) : 90.76177 90.57224 95.86651 assigned negative charge : -411.9073 centred at (gu) : 90.03448 90.09621 95.67410 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 78551 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22908 grid for indexing accessible points = 1.400000 m= 28409 mr = 55403 m= 4356 mr = 21090 m= 241 mr = 2713 m= 0 mr = 80 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 576 time to turn everything in is 0.6800000 number of dielectric boundary points 32271 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 20268 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) : 0.6353512 object centre at (A) : 12.64050 -1.667000 17.40200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.8512170E-02 -1.4256183E-02 midg,1,midg; midg,igrid,midg -1.0103160E-02 2.8410215E-02 1,midg,midg; igrid,midg,midg -7.3960121E-03 5.7825100E-02 gauss-seidel spectral radius is 0.9986483 estimated iterations to convergence 216 setup time was (sec) 0.9700000 now iterating at: 04:00:13 rms-change max change #iterations 4.411241 173.8373 at 10iterations 2.072596 69.62970 at 20iterations 0.9758847 39.50469 at 30iterations 0.4604942 14.26288 at 40iterations 0.2173691 7.171885 at 50iterations 0.1021623 3.756174 at 60iterations 4.8065893E-02 1.529757 at 70iterations 2.2694727E-02 0.7246857 at 80iterations 1.0668666E-02 0.3097801 at 90iterations 5.0239265E-03 0.1572514 at 100iterations 2.3729154E-03 7.3301315E-02 at 110iterations 1.1176582E-03 3.4566879E-02 at 120iterations finished qdiffx linear iterations at : 04:00:21 total time elapsed so far: 9.030000 # loops : 120 mean,max change (kT/e) : 1.1176582E-03 3.4566879E-02 energy calculations done at 9.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.210000 DelPhi exited at 04:00:22 9.212u 0.275s 0:10.03 94.5% 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 04:00:22 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 !!! WARNING: ARG 217 has a net charge of 1.2720 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.859080 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): -11.62600 36.90700 ymin,ymax (A): -25.80700 22.47300 zmin,zma (A): -10.61400 45.41800 x,y,z range (A): 48.53300 48.28000 56.03201 scale (grids/A): 2.859080 object centre (A): 12.64050 -1.667000 17.40200 number of atom coordinates read : 2726 total number of charged atoms : 2574 net assigned charge : 1.412011 assigned positive charge : 413.3188 centred at (gu) : 91.14249 90.85820 98.79975 assigned negative charge : -411.9073 centred at (gu) : 90.05173 90.14441 98.51108 start vw surface at 0.1600000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 181540 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22908 grid for indexing accessible points = 1.400000 m= 92447 mr = 133694 m= 32879 mr = 76087 m= 7680 mr = 26487 m= 1060 mr = 5808 m= 57 mr = 688 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 1825 time to turn everything in is 1.740000 number of dielectric boundary points 72868 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 20583 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) : 1.906054 object centre at (A) : 12.64050 -1.667000 17.40200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.002585 4.9336314E-02 midg,1,midg; midg,igrid,midg -0.1175776 0.3397602 1,midg,midg; igrid,midg,midg -9.8955147E-03 0.5454439 gauss-seidel spectral radius is 0.9992576 estimated iterations to convergence 290 setup time was (sec) 2.050000 now iterating at: 04:00:24 rms-change max change #iterations 10.28354 449.0696 at 10iterations 6.004872 143.1260 at 20iterations 3.497660 74.67474 at 30iterations 2.026965 49.10396 at 40iterations 1.173936 24.60092 at 50iterations 0.6781411 12.33881 at 60iterations 0.3918071 7.271008 at 70iterations 0.2260591 4.339100 at 80iterations 0.1302615 2.444167 at 90iterations 7.5179294E-02 1.252465 at 100iterations 4.3351721E-02 0.8448391 at 110iterations 2.4941076E-02 0.4472485 at 120iterations 1.4374853E-02 0.2770386 at 130iterations 8.3012581E-03 0.1526537 at 140iterations 4.8109749E-03 8.1462860E-02 at 150iterations 2.7949382E-03 5.3969383E-02 at 160iterations 1.6364875E-03 2.9159546E-02 at 170iterations 9.6956460E-04 1.7904758E-02 at 180iterations finished qdiffx linear iterations at : 04:00:38 total time elapsed so far: 15.32000 # loops : 180 mean,max change (kT/e) : 9.6956460E-04 1.7904758E-02 energy calculations done at 15.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.49000 DelPhi exited at 04:00:38 15.491u 0.289s 0:16.52 95.4% 0+0k 0+0io 0pf+0w