Mon Oct 10 14:01:30 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 14:01:30 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3373 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.5487476 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): -40.64000 16.55200 ymin,ymax (A): -13.50400 49.95600 zmin,zma (A): -51.59200 13.28300 x,y,z range (A): 57.19200 63.46000 64.87500 scale (grids/A): 0.5487476 object centre (A): -12.04400 18.22600 -19.15450 number of atom coordinates read : 3373 total number of charged atoms : 3230 net assigned charge : 13.22602 assigned positive charge : 499.4415 centred at (gu) : 89.81238 90.80048 91.37429 assigned negative charge : -486.2174 centred at (gu) : 89.92731 90.72835 91.55996 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6897 nv = 96 ne = 84 npr = 65221 no. pairs analyzed = 65221 no. exposed pairs = 4551 no. arc points = 33006 no. surface atoms = 1503 nbur = 1870 mkacc time = 0.1400000 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 = 1.540000 m= 262 mr = 3414 m= 0 mr = 10 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3735 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3329 ## 421 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8917 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7091862E-09 -8.6201685E-10 midg,1,midg; midg,igrid,midg 2.9242014E-10 1.8332089E-09 1,midg,midg; igrid,midg,midg 1.9296651E-09 -1.4273998E-12 gauss-seidel spectral radius is 0.9829218 estimated iterations to convergence 63 setup time was (sec) 0.5300000 now iterating at: 14:01:31 rms-change max change #iterations 7.7191971E-02 11.90524 at 10iterations 5.1717027E-03 0.8739796 at 20iterations 3.6998661E-04 6.9808960E-02 at 30iterations 3.1799125E-05 3.7879944E-03 at 40iterations 4.1493213E-06 4.3964386E-04 at 50iterations finished qdiffx linear iterations at : 14:01:33 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 4.1493213E-06 4.3964386E-04 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 14:01:34 3.119u 0.165s 0:04.39 74.4% 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 14:01:35 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3373 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.646243 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): -40.64000 16.55200 ymin,ymax (A): -13.50400 49.95600 zmin,zma (A): -51.59200 13.28300 x,y,z range (A): 57.19200 63.46000 64.87500 scale (grids/A): 1.646243 object centre (A): -12.04400 18.22600 -19.15450 number of atom coordinates read : 3373 total number of charged atoms : 3230 net assigned charge : 13.22602 assigned positive charge : 499.4415 centred at (gu) : 89.43619 92.40016 94.12167 assigned negative charge : -486.2174 centred at (gu) : 89.78156 92.18480 94.67938 start vw surface at 0.2500000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 75755 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33006 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23476 mr = 50085 m= 2482 mr = 15801 m= 74 mr = 1190 m= 0 mr = 5 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 569 time to turn everything in is 0.6100000 number of dielectric boundary points 34706 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 369 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 24781 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) : 0.5487476 object centre at (A) : -12.04400 18.22600 -19.15450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3311829E-02 8.8464711E-03 midg,1,midg; midg,igrid,midg 9.2080822E-03 3.4605116E-02 1,midg,midg; igrid,midg,midg 1.0595715E-02 -4.1696858E-03 gauss-seidel spectral radius is 0.9982746 estimated iterations to convergence 191 setup time was (sec) 0.8900000 now iterating at: 14:01:36 rms-change max change #iterations 3.580284 157.0277 at 10iterations 1.518347 55.90530 at 20iterations 0.6453533 25.88361 at 30iterations 0.2733449 8.659237 at 40iterations 0.1164961 4.129996 at 50iterations 4.9528241E-02 1.580444 at 60iterations 2.1080377E-02 0.7572956 at 70iterations 8.9858389E-03 0.3467922 at 80iterations 3.8197699E-03 0.1320801 at 90iterations 1.6338883E-03 5.2819252E-02 at 100iterations 6.9629488E-04 2.3147583E-02 at 110iterations 2.9854008E-04 9.9115372E-03 at 120iterations finished qdiffx linear iterations at : 14:01:42 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 2.9854008E-04 9.9115372E-03 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.430000 DelPhi exited at 14:01:43 7.431u 0.181s 0:08.28 91.9% 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 14:01:43 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3373 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.469364 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): -40.64000 16.55200 ymin,ymax (A): -13.50400 49.95600 zmin,zma (A): -51.59200 13.28300 x,y,z range (A): 57.19200 63.46000 64.87500 scale (grids/A): 2.469364 object centre (A): -12.04400 18.22600 -19.15450 number of atom coordinates read : 3373 total number of charged atoms : 3230 net assigned charge : 13.22602 assigned positive charge : 499.4415 centred at (gu) : 89.15411 93.59999 96.18239 assigned negative charge : -486.2174 centred at (gu) : 89.67234 93.27718 97.01907 start vw surface at 0.1600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 175986 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33006 grid for indexing accessible points = 1.400000 m= 80284 mr = 123093 m= 23450 mr = 62375 m= 3783 mr = 17476 m= 254 mr = 2432 m= 4 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 1783 time to turn everything in is 1.250000 number of dielectric boundary points 78284 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 25810 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) : 1.646243 object centre at (A) : -12.04400 18.22600 -19.15450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5312806 9.0906776E-02 midg,1,midg; midg,igrid,midg 0.3570430 0.5945533 1,midg,midg; igrid,midg,midg 0.1653856 -2.3838347E-02 gauss-seidel spectral radius is 0.9991844 estimated iterations to convergence 277 setup time was (sec) 1.540000 now iterating at: 14:01:45 rms-change max change #iterations 9.404333 319.7114 at 10iterations 5.425878 154.2240 at 20iterations 3.107930 76.06377 at 30iterations 1.768227 37.41895 at 40iterations 1.000305 22.90007 at 50iterations 0.5652025 11.99453 at 60iterations 0.3181088 6.386757 at 70iterations 0.1789630 3.804758 at 80iterations 0.1001311 1.925600 at 90iterations 5.6255899E-02 1.104683 at 100iterations 3.1513885E-02 0.6958313 at 110iterations 1.7650835E-02 0.3545389 at 120iterations 9.8518236E-03 0.2057266 at 130iterations 5.5139847E-03 0.1002197 at 140iterations 3.0790314E-03 6.1982393E-02 at 150iterations 1.7197060E-03 3.3893585E-02 at 160iterations 9.6317742E-04 2.0820618E-02 at 170iterations 5.3711474E-04 9.6626282E-03 at 180iterations finished qdiffx linear iterations at : 14:01:55 total time elapsed so far: 11.40000 # loops : 180 mean,max change (kT/e) : 5.3711474E-04 9.6626282E-03 energy calculations done at 11.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.57000 DelPhi exited at 14:01:56 11.573u 0.231s 0:13.12 89.9% 0+0k 0+0io 0pf+0w