Mon Oct 10 14:00:23 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 Mon Oct 10 2011 at 14:00:24 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4370 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5574085 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): 16.71300 78.76300 ymin,ymax (A): 119.5690 183.4360 zmin,zma (A): -1.102000 59.64600 x,y,z range (A): 62.05000 63.86699 60.74800 scale (grids/A): 0.5574085 object centre (A): 47.73800 151.5025 29.27200 number of atom coordinates read : 4370 total number of charged atoms : 4220 net assigned charge : 2.500044 assigned positive charge : 676.1272 centred at (gu) : 91.61791 89.28966 87.25603 assigned negative charge : -673.6302 centred at (gu) : 91.58320 89.18890 87.25011 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8856 nv = 96 ne = 84 npr = 87034 no. pairs analyzed = 87034 no. exposed pairs = 5281 no. arc points = 36891 no. surface atoms = 1774 nbur = 2596 mkacc time = 0.2300000 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 = 1.512000 m= 339 mr = 4784 m= 4 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.4600000 number of dielectric boundary points 4387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3716 ## 406 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 11485 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9285802E-10 1.7506582E-10 midg,1,midg; midg,igrid,midg -1.5480907E-09 1.4681912E-09 1,midg,midg; igrid,midg,midg -1.8688043E-10 1.1400164E-09 gauss-seidel spectral radius is 0.9835054 estimated iterations to convergence 64 setup time was (sec) 0.7600000 now iterating at: 14:00:25 rms-change max change #iterations 0.1004337 15.88921 at 10iterations 7.4741133E-03 1.253593 at 20iterations 7.2204549E-04 9.3084335E-02 at 30iterations 1.3678013E-04 1.8875122E-02 at 40iterations 3.4498622E-05 4.4202805E-03 at 50iterations finished qdiffx linear iterations at : 14:00:28 total time elapsed so far: 4.540000 # loops : 50 mean,max change (kT/e) : 3.4498622E-05 4.4202805E-03 energy calculations done at 4.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.710000 DelPhi exited at 14:00:29 4.711u 0.410s 0:05.81 88.1% 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 14:00:30 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4370 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.672225 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): 16.71300 78.76300 ymin,ymax (A): 119.5690 183.4360 zmin,zma (A): -1.102000 59.64600 x,y,z range (A): 62.05000 63.86699 60.74800 scale (grids/A): 1.672225 object centre (A): 47.73800 151.5025 29.27200 number of atom coordinates read : 4370 total number of charged atoms : 4220 net assigned charge : 2.500044 assigned positive charge : 676.1272 centred at (gu) : 94.85255 87.86834 81.76722 assigned negative charge : -673.6302 centred at (gu) : 94.74941 87.56651 81.74990 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 97925 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36891 grid for indexing accessible points = 1.400000 m= 31345 mr = 68428 m= 3852 mr = 21915 m= 139 mr = 2179 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 1407 time to turn everything in is 0.7900000 number of dielectric boundary points 40720 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 350 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 32441 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) : 0.5574085 object centre at (A) : 47.73800 151.5025 29.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2604168E-03 9.0685887E-03 midg,1,midg; midg,igrid,midg 2.5254892E-02 3.8246915E-02 1,midg,midg; igrid,midg,midg -1.2191386E-02 -1.9047873E-02 gauss-seidel spectral radius is 0.9984058 estimated iterations to convergence 199 setup time was (sec) 1.090000 now iterating at: 14:00:31 rms-change max change #iterations 4.457324 255.4448 at 10iterations 1.949495 81.97180 at 20iterations 0.8587279 32.90691 at 30iterations 0.3781997 13.94533 at 40iterations 0.1671630 5.197868 at 50iterations 7.3373377E-02 2.643639 at 60iterations 3.2423746E-02 1.449706 at 70iterations 1.4328760E-02 0.4213867 at 80iterations 6.3323202E-03 0.1824112 at 90iterations 2.8146026E-03 8.3118439E-02 at 100iterations 1.2548357E-03 3.9787292E-02 at 110iterations 5.6496408E-04 1.8163681E-02 at 120iterations finished qdiffx linear iterations at : 14:00:42 total time elapsed so far: 11.68000 # loops : 120 mean,max change (kT/e) : 5.6496408E-04 1.8163681E-02 energy calculations done at 11.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.83000 DelPhi exited at 14:00:43 11.835u 0.475s 0:13.70 89.7% 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 Mon Oct 10 2011 at 14:00:43 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4370 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.508338 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): 16.71300 78.76300 ymin,ymax (A): 119.5690 183.4360 zmin,zma (A): -1.102000 59.64600 x,y,z range (A): 62.05000 63.86699 60.74800 scale (grids/A): 2.508338 object centre (A): 47.73800 151.5025 29.27200 number of atom coordinates read : 4370 total number of charged atoms : 4220 net assigned charge : 2.500044 assigned positive charge : 676.1272 centred at (gu) : 97.27870 86.80227 77.65060 assigned negative charge : -673.6302 centred at (gu) : 97.12408 86.34963 77.62483 start vw surface at 0.1600000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 227673 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36891 grid for indexing accessible points = 1.400000 m= 106780 mr = 167117 m= 32784 mr = 85327 m= 6501 mr = 25147 m= 613 mr = 4681 m= 15 mr = 336 m= 0 mr = 0 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 4703 time to turn everything in is 1.970000 number of dielectric boundary points 91758 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 33729 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) : 1.672225 object centre at (A) : 47.73800 151.5025 29.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7301779E-02 0.1890223 midg,1,midg; midg,igrid,midg 0.4063372 0.6730965 1,midg,midg; igrid,midg,midg -0.1912501 -0.2903886 gauss-seidel spectral radius is 0.9992300 estimated iterations to convergence 284 setup time was (sec) 2.330000 now iterating at: 14:00:46 rms-change max change #iterations 11.22053 370.9690 at 10iterations 6.512722 143.5277 at 20iterations 3.755717 75.36112 at 30iterations 2.163631 41.68624 at 40iterations 1.237627 21.70602 at 50iterations 0.7082186 12.98210 at 60iterations 0.4048230 7.125062 at 70iterations 0.2306792 4.195143 at 80iterations 0.1312853 2.131500 at 90iterations 7.4896708E-02 1.215645 at 100iterations 4.2603642E-02 0.7424017 at 110iterations 2.4211660E-02 0.4019918 at 120iterations 1.3778014E-02 0.2422314 at 130iterations 7.8429570E-03 0.1382599 at 140iterations 4.4630538E-03 7.3987961E-02 at 150iterations 2.5378184E-03 4.6840668E-02 at 160iterations 1.4405852E-03 2.8812408E-02 at 170iterations 8.2289241E-04 1.4027357E-02 at 180iterations finished qdiffx linear iterations at : 14:01:04 total time elapsed so far: 19.89000 # loops : 180 mean,max change (kT/e) : 8.2289241E-04 1.4027357E-02 energy calculations done at 19.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.06000 DelPhi exited at 14:01:04 20.066u 0.469s 0:20.99 97.7% 0+0k 0+0io 0pf+0w