Mon Oct 10 16:08:54 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 16:08:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2185 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6568508 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): -22.63100 29.18800 ymin,ymax (A): -13.75800 40.44000 zmin,zma (A): -30.19300 11.86300 x,y,z range (A): 51.81900 54.19800 42.05600 scale (grids/A): 0.6568508 object centre (A): 3.278500 13.34100 -9.164999 number of atom coordinates read : 2185 total number of charged atoms : 2046 net assigned charge : 1.500006 assigned positive charge : 320.4225 centred at (gu) : 88.67832 88.63985 89.31475 assigned negative charge : -318.9230 centred at (gu) : 88.57747 88.67492 89.14053 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6584 nv = 96 ne = 84 npr = 43501 no. pairs analyzed = 43501 no. exposed pairs = 2826 no. arc points = 20278 no. surface atoms = 951 nbur = 1234 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 417 mr = 3518 m= 4 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3433 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1802 ## 143 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7448 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6238112E-08 2.5432685E-08 midg,1,midg; midg,igrid,midg 1.2086146E-08 -9.9932040E-10 1,midg,midg; igrid,midg,midg -1.5157431E-08 1.4221685E-08 gauss-seidel spectral radius is 0.9879585 estimated iterations to convergence 74 setup time was (sec) 0.6000000 now iterating at: 16:08:55 rms-change max change #iterations 0.1488884 23.96803 at 10iterations 1.5724242E-02 2.096027 at 20iterations 1.7720520E-03 0.2611485 at 30iterations 3.3270739E-04 5.1231384E-02 at 40iterations 1.2603035E-04 2.0459175E-02 at 50iterations finished qdiffx linear iterations at : 16:08:59 total time elapsed so far: 4.740000 # loops : 50 mean,max change (kT/e) : 1.2603035E-04 2.0459175E-02 energy calculations done at 4.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.900000 DelPhi exited at 16:09:00 4.909u 0.452s 0:05.65 94.6% 0+0k 0+0io 6pf+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 16:09:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2185 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.970552 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): -22.63100 29.18800 ymin,ymax (A): -13.75800 40.44000 zmin,zma (A): -30.19300 11.86300 x,y,z range (A): 51.81900 54.19800 42.05600 scale (grids/A): 1.970552 object centre (A): 3.278500 13.34100 -9.164999 number of atom coordinates read : 2185 total number of charged atoms : 2046 net assigned charge : 1.500006 assigned positive charge : 320.4225 centred at (gu) : 86.03461 85.91920 87.94406 assigned negative charge : -318.9230 centred at (gu) : 85.73235 86.02466 87.42154 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70570 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20278 grid for indexing accessible points = 1.400000 m= 26062 mr = 48208 m= 4493 mr = 18927 m= 379 mr = 2718 m= 5 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 31515 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 16164 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) : 0.6568508 object centre at (A) : 3.278500 13.34100 -9.164999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8229974E-02 2.9665075E-02 midg,1,midg; midg,igrid,midg 1.5764128E-02 1.0012412E-03 1,midg,midg; igrid,midg,midg -5.3174952E-03 -8.5818470E-03 gauss-seidel spectral radius is 0.9986845 estimated iterations to convergence 218 setup time was (sec) 0.9400000 now iterating at: 16:09:01 rms-change max change #iterations 4.128304 183.0738 at 10iterations 1.961845 73.99610 at 20iterations 0.9342625 30.02983 at 30iterations 0.4457402 14.30631 at 40iterations 0.2127293 7.542304 at 50iterations 0.1011037 3.287785 at 60iterations 4.8155192E-02 1.847880 at 70iterations 2.3046618E-02 0.7794480 at 80iterations 1.0997667E-02 0.3736835 at 90iterations 5.3118081E-03 0.1727114 at 100iterations 2.6178807E-03 8.6811066E-02 at 110iterations 1.3552828E-03 4.7893524E-02 at 120iterations finished qdiffx linear iterations at : 16:09:12 total time elapsed so far: 11.66000 # loops : 120 mean,max change (kT/e) : 1.3552828E-03 4.7893524E-02 energy calculations done at 11.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.83000 DelPhi exited at 16:09:13 11.839u 0.488s 0:12.59 97.7% 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 16:09:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2185 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.955828 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): -22.63100 29.18800 ymin,ymax (A): -13.75800 40.44000 zmin,zma (A): -30.19300 11.86300 x,y,z range (A): 51.81900 54.19800 42.05600 scale (grids/A): 2.955828 object centre (A): 3.278500 13.34100 -9.164999 number of atom coordinates read : 2185 total number of charged atoms : 2046 net assigned charge : 1.500006 assigned positive charge : 320.4225 centred at (gu) : 84.05190 83.87870 86.91608 assigned negative charge : -318.9230 centred at (gu) : 83.59857 84.03703 86.13228 start vw surface at 0.1000000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 162996 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20278 grid for indexing accessible points = 1.400000 m= 83566 mr = 116870 m= 30764 mr = 67807 m= 8160 mr = 24305 m= 1414 mr = 5893 m= 115 mr = 922 m= 2 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.580000 number of dielectric boundary points 71169 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 16367 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) : 1.970552 object centre at (A) : 3.278500 13.34100 -9.164999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1711187 0.3509492 midg,1,midg; midg,igrid,midg 0.1074783 -9.8036870E-02 1,midg,midg; igrid,midg,midg -0.1062821 -0.1459429 gauss-seidel spectral radius is 0.9992645 estimated iterations to convergence 291 setup time was (sec) 1.940000 now iterating at: 16:09:15 rms-change max change #iterations 9.360008 406.3349 at 10iterations 5.420181 120.8553 at 20iterations 3.140651 65.22323 at 30iterations 1.817675 35.21494 at 40iterations 1.048884 21.25761 at 50iterations 0.6069381 13.00367 at 60iterations 0.3490785 7.002061 at 70iterations 0.2014559 3.931303 at 80iterations 0.1163644 2.629945 at 90iterations 6.6860490E-02 1.228241 at 100iterations 3.8445402E-02 0.7388783 at 110iterations 2.2184851E-02 0.4155521 at 120iterations 1.2741357E-02 0.2305260 at 130iterations 7.3408117E-03 0.1418915 at 140iterations 4.2222980E-03 8.6237192E-02 at 150iterations 2.4320076E-03 4.7793388E-02 at 160iterations 1.4042725E-03 2.4093628E-02 at 170iterations 8.0867443E-04 1.8181562E-02 at 180iterations finished qdiffx linear iterations at : 16:09:33 total time elapsed so far: 19.82000 # loops : 180 mean,max change (kT/e) : 8.0867443E-04 1.8181562E-02 energy calculations done at 19.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.00000 DelPhi exited at 16:09:33 20.000u 0.530s 0:20.82 98.6% 0+0k 0+0io 0pf+0w