Tue Oct 11 03:50:44 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 03:50:44 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2775 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6621777 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): -9.674000 36.54400 ymin,ymax (A): -27.30400 21.51600 zmin,zma (A): -8.172000 45.59000 x,y,z range (A): 46.21800 48.82000 53.76200 scale (grids/A): 0.6621777 object centre (A): 13.43500 -2.894000 18.70900 number of atom coordinates read : 2775 total number of charged atoms : 2624 net assigned charge : 4.154016 assigned positive charge : 422.4197 centred at (gu) : 89.53773 90.71843 91.38848 assigned negative charge : -418.2663 centred at (gu) : 89.27908 90.59985 91.40424 start vw surface at 0.1200000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8112 nv = 96 ne = 84 npr = 56607 no. pairs analyzed = 56607 no. exposed pairs = 3293 no. arc points = 22743 no. surface atoms = 1108 nbur = 1667 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 469 mr = 4764 m= 1 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 36 time to turn everything in is 0.3300000 number of dielectric boundary points 3741 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2193 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9611 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1306795E-08 1.0330555E-08 midg,1,midg; midg,igrid,midg -1.3308079E-08 4.3858787E-08 1,midg,midg; igrid,midg,midg -5.3429126E-08 6.1741396E-08 gauss-seidel spectral radius is 0.9881889 estimated iterations to convergence 75 setup time was (sec) 0.6300000 now iterating at: 03:50:45 rms-change max change #iterations 0.1806815 30.88300 at 10iterations 1.9552834E-02 2.809677 at 20iterations 2.1403350E-03 0.2741699 at 30iterations 2.6340861E-04 2.9573441E-02 at 40iterations 4.7498183E-05 7.1983337E-03 at 50iterations finished qdiffx linear iterations at : 03:50:49 total time elapsed so far: 4.830000 # loops : 50 mean,max change (kT/e) : 4.7498183E-05 7.1983337E-03 energy calculations done at 4.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.010000 DelPhi exited at 03:50:50 5.014u 0.399s 0:05.87 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 Tue Oct 11 2011 at 03:50:50 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2775 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.986533 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): -9.674000 36.54400 ymin,ymax (A): -27.30400 21.51600 zmin,zma (A): -8.172000 45.59000 x,y,z range (A): 46.21800 48.82000 53.76200 scale (grids/A): 1.986533 object centre (A): 13.43500 -2.894000 18.70900 number of atom coordinates read : 2775 total number of charged atoms : 2624 net assigned charge : 4.154016 assigned positive charge : 422.4197 centred at (gu) : 88.61281 92.15441 94.16502 assigned negative charge : -418.2663 centred at (gu) : 87.83698 91.79943 94.21229 start vw surface at 0.1200000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 87368 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22743 grid for indexing accessible points = 1.400000 m= 33335 mr = 62568 m= 5490 mr = 25573 m= 376 mr = 3666 m= 7 mr = 185 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 1249 time to turn everything in is 0.7200000 number of dielectric boundary points 34584 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 20736 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) : 0.6621777 object centre at (A) : 13.43500 -2.894000 18.70900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0950395E-02 8.4038088E-03 midg,1,midg; midg,igrid,midg -1.4520271E-02 1.0914569E-02 1,midg,midg; igrid,midg,midg -2.9815573E-02 6.1728995E-02 gauss-seidel spectral radius is 0.9987519 estimated iterations to convergence 224 setup time was (sec) 1.040000 now iterating at: 03:50:51 rms-change max change #iterations 4.818289 213.2907 at 10iterations 2.342967 101.8252 at 20iterations 1.136306 34.36968 at 30iterations 0.5505443 18.98396 at 40iterations 0.2687118 7.688430 at 50iterations 0.1303756 3.830625 at 60iterations 6.3539438E-02 1.838339 at 70iterations 3.0796221E-02 0.8421783 at 80iterations 1.4948546E-02 0.4008675 at 90iterations 7.2795018E-03 0.2209635 at 100iterations 3.5389431E-03 0.1031895 at 110iterations 1.7376912E-03 4.9271584E-02 at 120iterations finished qdiffx linear iterations at : 03:51:02 total time elapsed so far: 11.26000 # loops : 120 mean,max change (kT/e) : 1.7376912E-03 4.9271584E-02 energy calculations done at 11.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.44000 DelPhi exited at 03:51:02 11.441u 0.446s 0:12.32 96.4% 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 Tue Oct 11 2011 at 03:51:02 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2775 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.979800 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): -9.674000 36.54400 ymin,ymax (A): -27.30400 21.51600 zmin,zma (A): -8.172000 45.59000 x,y,z range (A): 46.21800 48.82000 53.76200 scale (grids/A): 2.979800 object centre (A): 13.43500 -2.894000 18.70900 number of atom coordinates read : 2775 total number of charged atoms : 2624 net assigned charge : 4.154016 assigned positive charge : 422.4197 centred at (gu) : 87.91901 93.23159 96.24738 assigned negative charge : -418.2663 centred at (gu) : 86.75536 92.69905 96.31845 start vw surface at 0.1100000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 201776 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22743 grid for indexing accessible points = 1.400000 m= 106903 mr = 150675 m= 40282 mr = 89678 m= 10140 mr = 33267 m= 1667 mr = 7956 m= 135 mr = 1278 m= 1 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 3968 time to turn everything in is 1.950000 number of dielectric boundary points 77979 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 20984 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) : 1.986533 object centre at (A) : 13.43500 -2.894000 18.70900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2063783 0.2586276 midg,1,midg; midg,igrid,midg -0.1708538 8.7950051E-02 1,midg,midg; igrid,midg,midg -0.2560634 0.5142679 gauss-seidel spectral radius is 0.9992861 estimated iterations to convergence 295 setup time was (sec) 2.330000 now iterating at: 03:51:05 rms-change max change #iterations 11.00562 342.5479 at 10iterations 6.470984 139.7673 at 20iterations 3.784152 63.03563 at 30iterations 2.212566 40.62448 at 40iterations 1.291406 23.88689 at 50iterations 0.7546811 13.50870 at 60iterations 0.4394477 8.887238 at 70iterations 0.2564799 4.286203 at 80iterations 0.1488904 2.592529 at 90iterations 8.6833313E-02 1.636586 at 100iterations 5.0556362E-02 0.8740177 at 110iterations 2.9302340E-02 0.4833852 at 120iterations 1.7062228E-02 0.2723255 at 130iterations 9.9109979E-03 0.1586914 at 140iterations 5.7696630E-03 9.1510773E-02 at 150iterations 3.3515333E-03 5.4227829E-02 at 160iterations 1.9561583E-03 3.2672882E-02 at 170iterations 1.1401091E-03 1.9941330E-02 at 180iterations finished qdiffx linear iterations at : 03:51:23 total time elapsed so far: 20.47000 # loops : 180 mean,max change (kT/e) : 1.1401091E-03 1.9941330E-02 energy calculations done at 20.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.65000 DelPhi exited at 03:51:24 20.654u 0.465s 0:21.64 97.5% 0+0k 0+0io 0pf+0w