Mon Oct 10 14:26:31 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 14:26:31 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 = 2612 !!! WARNING: HIT 362 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6041579 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): -3.169000 55.75600 ymin,ymax (A): -11.63100 44.57400 zmin,zma (A): -11.31100 46.00100 x,y,z range (A): 58.92500 56.20500 57.31200 scale (grids/A): 0.6041579 object centre (A): 26.29350 16.47150 17.34500 number of atom coordinates read : 2612 total number of charged atoms : 2463 net assigned charge : -2.985995 assigned positive charge : 393.7429 centred at (gu) : 92.41800 91.47250 89.23579 assigned negative charge : -396.7295 centred at (gu) : 92.23607 91.44456 89.24575 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6257 nv = 96 ne = 84 npr = 52490 no. pairs analyzed = 52490 no. exposed pairs = 3552 no. arc points = 24652 no. surface atoms = 1193 nbur = 1419 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 292 mr = 3064 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3100000 number of dielectric boundary points 3463 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2486 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7835 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4799076E-09 -1.7665774E-09 midg,1,midg; midg,igrid,midg -2.0551760E-09 -6.7079792E-10 1,midg,midg; igrid,midg,midg -5.5023235E-09 1.0286437E-08 gauss-seidel spectral radius is 0.9858230 estimated iterations to convergence 69 setup time was (sec) 0.5700000 now iterating at: 14:26:32 rms-change max change #iterations 0.1165949 21.00940 at 10iterations 9.8140612E-03 1.418638 at 20iterations 8.4336486E-04 0.1234341 at 30iterations 7.5961034E-05 1.3256073E-02 at 40iterations 6.9300072E-06 1.0814667E-03 at 50iterations finished qdiffx linear iterations at : 14:26:35 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 6.9300072E-06 1.0814667E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 14:26:35 3.544u 0.180s 0:04.31 86.3% 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 14:26:35 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2612 !!! WARNING: HIT 362 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.812474 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): -3.169000 55.75600 ymin,ymax (A): -11.63100 44.57400 zmin,zma (A): -11.31100 46.00100 x,y,z range (A): 58.92500 56.20500 57.31200 scale (grids/A): 1.812474 object centre (A): 26.29350 16.47150 17.34500 number of atom coordinates read : 2612 total number of charged atoms : 2463 net assigned charge : -2.985995 assigned positive charge : 393.7429 centred at (gu) : 97.25317 94.41668 87.70683 assigned negative charge : -396.7295 centred at (gu) : 96.70806 94.33348 87.73685 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 67715 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24652 grid for indexing accessible points = 1.400000 m= 21549 mr = 44479 m= 2818 mr = 14501 m= 166 mr = 1471 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 31745 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 184 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19233 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) : 0.6041579 object centre at (A) : 26.29350 16.47150 17.34500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4012778E-02 -6.7549092E-03 midg,1,midg; midg,igrid,midg -2.6290148E-02 -3.3189468E-02 1,midg,midg; igrid,midg,midg -1.4903851E-02 6.3047916E-02 gauss-seidel spectral radius is 0.9984917 estimated iterations to convergence 204 setup time was (sec) 0.8200000 now iterating at: 14:26:36 rms-change max change #iterations 3.915920 201.3715 at 10iterations 1.756305 76.82979 at 20iterations 0.7902426 26.04767 at 30iterations 0.3527668 11.35918 at 40iterations 0.1592634 5.105765 at 50iterations 7.1565352E-02 2.410945 at 60iterations 3.2119226E-02 1.115937 at 70iterations 1.4485669E-02 0.4940491 at 80iterations 6.5228166E-03 0.2394073 at 90iterations 2.9288265E-03 0.1030121 at 100iterations 1.3257702E-03 4.8298359E-02 at 110iterations 5.9704442E-04 2.1374702E-02 at 120iterations finished qdiffx linear iterations at : 14:26:43 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 5.9704442E-04 2.1374702E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 14:26:44 7.931u 0.240s 0:08.75 93.3% 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 14:26:44 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 = 2612 !!! WARNING: HIT 362 has a net charge of 0.5140 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: 2.718710 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): -3.169000 55.75600 ymin,ymax (A): -11.63100 44.57400 zmin,zma (A): -11.31100 46.00100 x,y,z range (A): 58.92500 56.20500 57.31200 scale (grids/A): 2.718710 object centre (A): 26.29350 16.47150 17.34500 number of atom coordinates read : 2612 total number of charged atoms : 2463 net assigned charge : -2.985995 assigned positive charge : 393.7429 centred at (gu) : 100.8796 96.62500 86.56004 assigned negative charge : -396.7295 centred at (gu) : 100.0621 96.50013 86.60531 start vw surface at 0.1600000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 156934 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24652 grid for indexing accessible points = 1.400000 m= 72311 mr = 109075 m= 23012 mr = 56299 m= 4797 mr = 17064 m= 669 mr = 3156 m= 37 mr = 437 m= 0 mr = 11 time to grow re-entrant surface = 0.7399999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.320000 number of dielectric boundary points 71718 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 19699 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) : 1.812474 object centre at (A) : 26.29350 16.47150 17.34500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3092763 -8.7227337E-02 midg,1,midg; midg,igrid,midg -0.3379951 -0.3527259 1,midg,midg; igrid,midg,midg -3.4344573E-02 1.318104 gauss-seidel spectral radius is 0.9992291 estimated iterations to convergence 284 setup time was (sec) 1.630000 now iterating at: 14:26:46 rms-change max change #iterations 9.437424 272.1891 at 10iterations 5.469689 121.6206 at 20iterations 3.147852 77.05220 at 30iterations 1.802184 37.59352 at 40iterations 1.028687 21.64109 at 50iterations 0.5854616 13.54014 at 60iterations 0.3342554 6.597194 at 70iterations 0.1896611 4.286055 at 80iterations 0.1080889 2.107514 at 90iterations 6.1325960E-02 1.168338 at 100iterations 3.4854613E-02 0.6975327 at 110iterations 1.9767119E-02 0.3623573 at 120iterations 1.1219194E-02 0.2198248 at 130iterations 6.3802977E-03 0.1239052 at 140iterations 3.6113637E-03 6.8475962E-02 at 150iterations 2.0520212E-03 4.3663025E-02 at 160iterations 1.1666549E-03 2.3237348E-02 at 170iterations 6.6324673E-04 1.3565063E-02 at 180iterations finished qdiffx linear iterations at : 14:26:57 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 6.6324673E-04 1.3565063E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 14:26:58 12.814u 0.253s 0:13.80 94.6% 0+0k 0+0io 0pf+0w