Mon Oct 10 19:50:36 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 19:50:36 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2607 !!! WARNING: HIR 107 has a net charge of 0.5140 !!! WARNING: HIR 233 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: 0.6193674 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): -11.98100 45.49700 ymin,ymax (A): -17.18700 36.43100 zmin,zma (A): -11.97100 45.37600 x,y,z range (A): 57.47800 53.61800 57.34700 scale (grids/A): 0.6193674 object centre (A): 16.75800 9.622000 16.70250 number of atom coordinates read : 2607 total number of charged atoms : 2469 net assigned charge : -1.971987 assigned positive charge : 388.6428 centred at (gu) : 89.66310 90.41702 90.40318 assigned negative charge : -390.6159 centred at (gu) : 89.67388 90.46514 90.36430 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6826 nv = 96 ne = 84 npr = 51768 no. pairs analyzed = 51768 no. exposed pairs = 3619 no. arc points = 25895 no. surface atoms = 1203 nbur = 1404 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 389 mr = 3332 m= 6 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3852 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2583 ## 242 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8268 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7716856E-09 1.0886422E-09 midg,1,midg; midg,igrid,midg 1.4402645E-09 -5.1934963E-09 1,midg,midg; igrid,midg,midg -9.0889607E-10 -2.1060305E-09 gauss-seidel spectral radius is 0.9865172 estimated iterations to convergence 71 setup time was (sec) 0.7000000 now iterating at: 19:50:37 rms-change max change #iterations 0.1223448 17.30423 at 10iterations 1.1196830E-02 1.718132 at 20iterations 1.0128687E-03 0.1499557 at 30iterations 9.2832488E-05 1.2880325E-02 at 40iterations 8.6636892E-06 1.1491776E-03 at 50iterations finished qdiffx linear iterations at : 19:50:41 total time elapsed so far: 4.320000 # loops : 50 mean,max change (kT/e) : 8.6636892E-06 1.1491776E-03 energy calculations done at 4.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.530000 DelPhi exited at 19:50:42 4.535u 0.422s 0:05.23 94.6% 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 19:50:42 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2607 !!! WARNING: HIR 107 has a net charge of 0.5140 !!! WARNING: HIR 233 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: 1.858102 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): -11.98100 45.49700 ymin,ymax (A): -17.18700 36.43100 zmin,zma (A): -11.97100 45.37600 x,y,z range (A): 57.47800 53.61800 57.34700 scale (grids/A): 1.858102 object centre (A): 16.75800 9.622000 16.70250 number of atom coordinates read : 2607 total number of charged atoms : 2469 net assigned charge : -1.971987 assigned positive charge : 388.6428 centred at (gu) : 88.98887 91.25050 91.20863 assigned negative charge : -390.6159 centred at (gu) : 89.02142 91.39527 91.09276 start vw surface at 0.1400000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 73220 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25895 grid for indexing accessible points = 1.400000 m= 25275 mr = 47593 m= 4008 mr = 17527 m= 240 mr = 2245 m= 1 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 35313 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 19329 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) : 0.6193674 object centre at (A) : 16.75800 9.622000 16.70250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5582445E-02 -3.4006178E-02 midg,1,midg; midg,igrid,midg 1.8322997E-02 -1.6114685E-03 1,midg,midg; igrid,midg,midg 1.4567581E-02 -4.6518007E-03 gauss-seidel spectral radius is 0.9985931 estimated iterations to convergence 211 setup time was (sec) 1.090000 now iterating at: 19:50:43 rms-change max change #iterations 4.075924 194.8279 at 10iterations 1.870046 64.33585 at 20iterations 0.8643156 31.07619 at 30iterations 0.3980901 13.40650 at 40iterations 0.1835002 6.364094 at 50iterations 8.4780656E-02 3.113348 at 60iterations 3.9246276E-02 1.163422 at 70iterations 1.8138934E-02 0.5778694 at 80iterations 8.3927764E-03 0.2776222 at 90iterations 3.8739694E-03 0.1275749 at 100iterations 1.7861668E-03 5.9940338E-02 at 110iterations 8.2879025E-04 2.6528835E-02 at 120iterations finished qdiffx linear iterations at : 19:50:53 total time elapsed so far: 10.49000 # loops : 120 mean,max change (kT/e) : 8.2879025E-04 2.6528835E-02 energy calculations done at 10.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.70000 DelPhi exited at 19:50:53 10.704u 0.457s 0:11.69 95.3% 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 19:50:53 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2607 !!! WARNING: HIR 107 has a net charge of 0.5140 !!! WARNING: HIR 233 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: 2.787153 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): -11.98100 45.49700 ymin,ymax (A): -17.18700 36.43100 zmin,zma (A): -11.97100 45.37600 x,y,z range (A): 57.47800 53.61800 57.34700 scale (grids/A): 2.787153 object centre (A): 16.75800 9.622000 16.70250 number of atom coordinates read : 2607 total number of charged atoms : 2469 net assigned charge : -1.971987 assigned positive charge : 388.6428 centred at (gu) : 88.48325 91.87560 91.81285 assigned negative charge : -390.6159 centred at (gu) : 88.53220 92.09292 91.63916 start vw surface at 0.1600000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 169216 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25895 grid for indexing accessible points = 1.400000 m= 81424 mr = 116545 m= 29407 mr = 63885 m= 7139 mr = 22596 m= 958 mr = 4958 m= 48 mr = 511 m= 0 mr = 12 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.010000 number of dielectric boundary points 79685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.170000 number of grid points assigned charge 19751 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) : 1.858102 object centre at (A) : 16.75800 9.622000 16.70250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1023043 -0.3532319 midg,1,midg; midg,igrid,midg 0.2482101 0.1352881 1,midg,midg; igrid,midg,midg 0.1971246 -7.6533660E-02 gauss-seidel spectral radius is 0.9992600 estimated iterations to convergence 290 setup time was (sec) 2.380000 now iterating at: 19:50:56 rms-change max change #iterations 9.889258 405.0892 at 10iterations 5.847991 147.3539 at 20iterations 3.425890 86.03838 at 30iterations 1.996614 44.13473 at 40iterations 1.161523 25.50274 at 50iterations 0.6730801 14.19004 at 60iterations 0.3886924 7.696578 at 70iterations 0.2244621 4.417575 at 80iterations 0.1293121 2.524677 at 90iterations 7.4654303E-02 1.767838 at 100iterations 4.2917889E-02 0.7956400 at 110iterations 2.4708906E-02 0.4576645 at 120iterations 1.4211001E-02 0.2624276 at 130iterations 8.1602754E-03 0.1601830 at 140iterations 4.6893354E-03 8.7059021E-02 at 150iterations 2.6939323E-03 4.6852112E-02 at 160iterations 1.5491896E-03 2.7591705E-02 at 170iterations 8.8918745E-04 1.8337250E-02 at 180iterations finished qdiffx linear iterations at : 19:51:12 total time elapsed so far: 18.20000 # loops : 180 mean,max change (kT/e) : 8.8918745E-04 1.8337250E-02 energy calculations done at 18.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.42000 DelPhi exited at 19:51:13 18.427u 0.465s 0:19.18 98.4% 0+0k 0+0io 0pf+0w