Tue Oct 11 06:44:26 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 Tue Oct 11 2011 at 06:44:26 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 = 2019 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7021835 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): 3.437000 45.96300 ymin,ymax (A): 0.5340000 41.26300 zmin,zma (A): -3.584000 47.11500 x,y,z range (A): 42.52600 40.72900 50.69900 scale (grids/A): 0.7021835 object centre (A): 24.70000 20.89850 21.76550 number of atom coordinates read : 2019 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 90.39265 90.35601 90.64431 assigned negative charge : -305.3172 centred at (gu) : 90.58005 90.32310 90.67911 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6853 nv = 96 ne = 84 npr = 39654 no. pairs analyzed = 39654 no. exposed pairs = 2451 no. arc points = 17026 no. surface atoms = 831 nbur = 1188 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 440 mr = 3925 m= 2 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1635 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7698 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.2965391E-08 4.6550216E-08 midg,1,midg; midg,igrid,midg 3.9436415E-08 7.5388208E-08 1,midg,midg; igrid,midg,midg 1.2534522E-07 -2.8181674E-08 gauss-seidel spectral radius is 0.9894246 estimated iterations to convergence 79 setup time was (sec) 0.5400000 now iterating at: 06:44:27 rms-change max change #iterations 0.1861762 28.51105 at 10iterations 2.3273295E-02 3.486515 at 20iterations 2.9130820E-03 0.4089928 at 30iterations 4.1282395E-04 6.0019016E-02 at 40iterations 8.2286228E-05 1.2166977E-02 at 50iterations finished qdiffx linear iterations at : 06:44:31 total time elapsed so far: 4.210000 # loops : 50 mean,max change (kT/e) : 8.2286228E-05 1.2166977E-02 energy calculations done at 4.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 06:44:31 4.407u 0.285s 0:05.01 93.4% 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 06:44:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2019 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: 2.106550 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): 3.437000 45.96300 ymin,ymax (A): 0.5340000 41.26300 zmin,zma (A): -3.584000 47.11500 x,y,z range (A): 42.52600 40.72900 50.69900 scale (grids/A): 2.106550 object centre (A): 24.70000 20.89850 21.76550 number of atom coordinates read : 2019 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 91.17810 91.06807 91.93285 assigned negative charge : -305.3172 centred at (gu) : 91.74007 90.96958 92.03754 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 72637 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17026 grid for indexing accessible points = 1.400000 m= 28717 mr = 51609 m= 5607 mr = 21790 m= 531 mr = 3753 m= 8 mr = 265 m= 0 mr = 2 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 30081 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 101 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 15380 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) : 0.7021835 object centre at (A) : 24.70000 20.89850 21.76550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4894740E-02 6.4522222E-02 midg,1,midg; midg,igrid,midg 4.0606791E-03 3.1936385E-02 1,midg,midg; igrid,midg,midg 4.1129455E-02 1.3714856E-02 gauss-seidel spectral radius is 0.9988105 estimated iterations to convergence 230 setup time was (sec) 0.9500000 now iterating at: 06:44:32 rms-change max change #iterations 4.479950 217.4820 at 10iterations 2.202638 70.76834 at 20iterations 1.087115 32.82684 at 30iterations 0.5383378 17.05056 at 40iterations 0.2660907 8.128416 at 50iterations 0.1313080 4.066437 at 60iterations 6.4917795E-02 1.978752 at 70iterations 3.2015894E-02 1.016379 at 80iterations 1.5824510E-02 0.5039368 at 90iterations 7.8677647E-03 0.2493706 at 100iterations 3.9257798E-03 0.1377640 at 110iterations 1.9807713E-03 5.9210777E-02 at 120iterations finished qdiffx linear iterations at : 06:44:41 total time elapsed so far: 9.930000 # loops : 120 mean,max change (kT/e) : 1.9807713E-03 5.9210777E-02 energy calculations done at 9.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.12000 DelPhi exited at 06:44:42 10.121u 0.341s 0:10.87 96.2% 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 06:44:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2019 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.159826 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): 3.437000 45.96300 ymin,ymax (A): 0.5340000 41.26300 zmin,zma (A): -3.584000 47.11500 x,y,z range (A): 42.52600 40.72900 50.69900 scale (grids/A): 3.159826 object centre (A): 24.70000 20.89850 21.76550 number of atom coordinates read : 2019 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 91.76707 91.60205 92.89919 assigned negative charge : -305.3172 centred at (gu) : 92.61008 91.45428 93.05624 start vw surface at 0.1200000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 167439 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17026 grid for indexing accessible points = 1.400000 m= 90563 mr = 124400 m= 36099 mr = 75332 m= 10544 mr = 29699 m= 2059 mr = 8078 m= 201 mr = 1507 m= 7 mr = 128 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.820000 number of dielectric boundary points 67768 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 15496 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) : 2.106550 object centre at (A) : 24.70000 20.89850 21.76550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3777041 0.6718726 midg,1,midg; midg,igrid,midg -6.2862127E-03 0.2474469 1,midg,midg; igrid,midg,midg 0.3288971 0.3215033 gauss-seidel spectral radius is 0.9992881 estimated iterations to convergence 296 setup time was (sec) 2.200000 now iterating at: 06:44:45 rms-change max change #iterations 10.03693 437.7844 at 10iterations 5.910185 144.3387 at 20iterations 3.483876 68.06094 at 30iterations 2.049351 45.26797 at 40iterations 1.199994 22.31051 at 50iterations 0.7044926 13.97009 at 60iterations 0.4116073 8.331676 at 70iterations 0.2403320 4.140670 at 80iterations 0.1405183 2.434655 at 90iterations 8.2249098E-02 1.810020 at 100iterations 4.7888238E-02 0.8519759 at 110iterations 2.8098948E-02 0.4922085 at 120iterations 1.6468082E-02 0.2932774 at 130iterations 9.7084520E-03 0.2070363 at 140iterations 5.7948851E-03 0.1029015 at 150iterations 3.5088721E-03 6.3848495E-02 at 160iterations 2.2030247E-03 4.2785645E-02 at 170iterations 1.4405925E-03 2.4429321E-02 at 180iterations finished qdiffx linear iterations at : 06:44:59 total time elapsed so far: 16.69000 # loops : 180 mean,max change (kT/e) : 1.4405925E-03 2.4429321E-02 energy calculations done at 16.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.87000 DelPhi exited at 06:45:00 16.876u 0.371s 0:17.56 98.1% 0+0k 0+0io 0pf+0w