Tue Oct 11 06:00:13 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 06:00:14 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 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: 0.7094460 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): 25.87700 72.35300 ymin,ymax (A): -18.67600 31.50400 zmin,zma (A): 4.128000 46.59000 x,y,z range (A): 46.47600 50.18000 42.46200 scale (grids/A): 0.7094460 object centre (A): 49.11500 6.414001 25.35900 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 89.25018 90.20102 90.26978 assigned negative charge : -318.8441 centred at (gu) : 89.38573 90.15089 90.35413 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7243 nv = 96 ne = 84 npr = 42452 no. pairs analyzed = 42452 no. exposed pairs = 2607 no. arc points = 17829 no. surface atoms = 897 nbur = 1430 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 498 mr = 4178 m= 1 mr = 95 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 0.2700000 number of dielectric boundary points 3469 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1638 ## 140 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8019 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.6116963E-08 1.2551193E-08 midg,1,midg; midg,igrid,midg 2.9350799E-08 8.6652904E-08 1,midg,midg; igrid,midg,midg 1.4777838E-07 -1.2974353E-08 gauss-seidel spectral radius is 0.9896468 estimated iterations to convergence 80 setup time was (sec) 0.5200000 now iterating at: 06:00:14 rms-change max change #iterations 0.2014762 38.12403 at 10iterations 2.5378354E-02 3.590702 at 20iterations 3.3684860E-03 0.4408979 at 30iterations 5.9170602E-04 7.5043678E-02 at 40iterations 1.6094361E-04 2.0915985E-02 at 50iterations finished qdiffx linear iterations at : 06:00:17 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.6094361E-04 2.0915985E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 06:00:17 3.396u 0.190s 0:03.92 91.3% 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 Tue Oct 11 2011 at 06:00:17 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 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: 2.128338 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): 25.87700 72.35300 ymin,ymax (A): -18.67600 31.50400 zmin,zma (A): 4.128000 46.59000 x,y,z range (A): 46.47600 50.18000 42.46200 scale (grids/A): 2.128338 object centre (A): 49.11500 6.414001 25.35900 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 87.75051 90.60308 90.80944 assigned negative charge : -318.8441 centred at (gu) : 88.15727 90.45284 91.06238 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 76977 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17829 grid for indexing accessible points = 1.400000 m= 31570 mr = 54883 m= 6218 mr = 24134 m= 559 mr = 4102 m= 18 mr = 280 m= 0 mr = 3 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 31940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 15893 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) : 0.7094460 object centre at (A) : 49.11500 6.414001 25.35900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2149248E-02 2.9633168E-02 midg,1,midg; midg,igrid,midg 4.6864212E-02 2.8064521E-02 1,midg,midg; igrid,midg,midg 4.6385933E-02 -5.0802834E-02 gauss-seidel spectral radius is 0.9988419 estimated iterations to convergence 233 setup time was (sec) 0.9100000 now iterating at: 06:00:19 rms-change max change #iterations 4.647867 209.6102 at 10iterations 2.307859 75.94646 at 20iterations 1.147799 36.91924 at 30iterations 0.5695361 18.41843 at 40iterations 0.2847401 8.605371 at 50iterations 0.1420777 4.170208 at 60iterations 7.0751123E-02 2.091995 at 70iterations 3.5245821E-02 1.176054 at 80iterations 1.7624119E-02 0.5241871 at 90iterations 8.8545978E-03 0.2699099 at 100iterations 4.4738250E-03 0.1319742 at 110iterations 2.3098721E-03 6.6915989E-02 at 120iterations finished qdiffx linear iterations at : 06:00:26 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 2.3098721E-03 6.6915989E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.270000 DelPhi exited at 06:00:26 8.274u 0.233s 0:08.99 94.5% 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 06:00:27 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 3.192507 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): 25.87700 72.35300 ymin,ymax (A): -18.67600 31.50400 zmin,zma (A): 4.128000 46.59000 x,y,z range (A): 46.47600 50.18000 42.46200 scale (grids/A): 3.192507 object centre (A): 49.11500 6.414001 25.35900 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 86.62582 90.90463 91.21420 assigned negative charge : -318.8441 centred at (gu) : 87.23583 90.67928 91.59357 start vw surface at 0.1600000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 177509 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17829 grid for indexing accessible points = 1.400000 m= 98037 mr = 132118 m= 40314 mr = 81882 m= 11618 mr = 33211 m= 2405 mr = 9027 m= 317 mr = 1714 m= 23 mr = 203 m= 0 mr = 9 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.830000 number of dielectric boundary points 72059 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 16016 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) : 2.128338 object centre at (A) : 49.11500 6.414001 25.35900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1262933 0.2391196 midg,1,midg; midg,igrid,midg 0.3874514 0.1374674 1,midg,midg; igrid,midg,midg 0.4452643 -0.6347275 gauss-seidel spectral radius is 0.9992999 estimated iterations to convergence 298 setup time was (sec) 2.150000 now iterating at: 06:00:29 rms-change max change #iterations 10.36908 354.8630 at 10iterations 6.157535 136.8224 at 20iterations 3.654305 78.07500 at 30iterations 2.158429 41.29834 at 40iterations 1.274085 29.25166 at 50iterations 0.7499623 13.78360 at 60iterations 0.4419379 8.998493 at 70iterations 0.2599774 4.770321 at 80iterations 0.1527153 3.043541 at 90iterations 8.9713529E-02 1.641024 at 100iterations 5.2777532E-02 0.9371014 at 110iterations 3.1203633E-02 0.5801964 at 120iterations 1.8515579E-02 0.3509612 at 130iterations 1.1132186E-02 0.1926795 at 140iterations 6.8656318E-03 0.1329002 at 150iterations 4.3646134E-03 8.0783844E-02 at 160iterations 2.9308284E-03 5.5973053E-02 at 170iterations 2.0902974E-03 3.9024353E-02 at 180iterations finished qdiffx linear iterations at : 06:00:40 total time elapsed so far: 12.78000 # loops : 180 mean,max change (kT/e) : 2.0902974E-03 3.9024353E-02 energy calculations done at 12.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.96000 DelPhi exited at 06:00:40 12.960u 0.256s 0:13.53 97.6% 0+0k 0+0io 0pf+0w