Tue Oct 11 03:21:30 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 03:21:30 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1797 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7238568 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): 18.46300 64.02900 ymin,ymax (A): -10.98900 34.07100 zmin,zma (A): 0.2840000 49.46500 x,y,z range (A): 45.56600 45.06000 49.18100 scale (grids/A): 0.7238568 object centre (A): 41.24600 11.54100 24.87450 number of atom coordinates read : 1797 total number of charged atoms : 1631 net assigned charge : 7.000008 assigned positive charge : 266.6172 centred at (gu) : 91.15097 90.65995 90.27332 assigned negative charge : -259.6174 centred at (gu) : 91.23983 91.09530 90.31339 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6477 nv = 96 ne = 84 npr = 35042 no. pairs analyzed = 35042 no. exposed pairs = 2416 no. arc points = 17090 no. surface atoms = 813 nbur = 984 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 425 mr = 3400 m= 3 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 49 time to turn everything in is 0.1600000 number of dielectric boundary points 3452 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1419 ## 122 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 6692 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0730643E-07 6.9204788E-08 midg,1,midg; midg,igrid,midg 2.9478070E-07 -2.0277358E-07 1,midg,midg; igrid,midg,midg 1.1384162E-07 4.4754664E-08 gauss-seidel spectral radius is 0.9900274 estimated iterations to convergence 81 setup time was (sec) 0.3400000 now iterating at: 03:21:31 rms-change max change #iterations 0.2028716 42.44644 at 10iterations 2.5470162E-02 3.526265 at 20iterations 3.2723516E-03 0.4804707 at 30iterations 4.2281026E-04 6.4075470E-02 at 40iterations 5.3178537E-05 8.2073212E-03 at 50iterations finished qdiffx linear iterations at : 03:21:34 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 5.3178537E-05 8.2073212E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 03:21:34 3.333u 0.157s 0:03.97 87.6% 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 Tue Oct 11 2011 at 03:21:34 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1797 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.171570 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): 18.46300 64.02900 ymin,ymax (A): -10.98900 34.07100 zmin,zma (A): 0.2840000 49.46500 x,y,z range (A): 45.56600 45.06000 49.18100 scale (grids/A): 2.171570 object centre (A): 41.24600 11.54100 24.87450 number of atom coordinates read : 1797 total number of charged atoms : 1631 net assigned charge : 7.000008 assigned positive charge : 266.6172 centred at (gu) : 93.45276 91.98008 90.82018 assigned negative charge : -259.6174 centred at (gu) : 93.71972 93.28621 90.94051 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 67567 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17090 grid for indexing accessible points = 1.400000 m= 26540 mr = 44948 m= 4937 mr = 19606 m= 497 mr = 2933 m= 22 mr = 221 m= 0 mr = 2 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1126 time to turn everything in is 0.3600000 number of dielectric boundary points 31853 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 12978 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) : 0.7238568 object centre at (A) : 41.24600 11.54100 24.87450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2327912E-02 5.9787412E-03 midg,1,midg; midg,igrid,midg 8.2577646E-02 -9.4563961E-02 1,midg,midg; igrid,midg,midg 2.3747291E-02 5.9103865E-02 gauss-seidel spectral radius is 0.9988596 estimated iterations to convergence 234 setup time was (sec) 0.5800000 now iterating at: 03:21:35 rms-change max change #iterations 4.399433 221.8430 at 10iterations 2.195990 87.22733 at 20iterations 1.092353 38.75946 at 30iterations 0.5451702 20.19811 at 40iterations 0.2725350 9.548859 at 50iterations 0.1361485 4.181436 at 60iterations 6.7666911E-02 1.995085 at 70iterations 3.3853933E-02 1.034277 at 80iterations 1.6836204E-02 0.5176699 at 90iterations 8.4054042E-03 0.2683859 at 100iterations 4.2012013E-03 0.1313572 at 110iterations 2.1045427E-03 6.8256855E-02 at 120iterations finished qdiffx linear iterations at : 03:21:42 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 2.1045427E-03 6.8256855E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 03:21:42 7.907u 0.193s 0:08.39 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 03:21:43 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1797 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.257355 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): 18.46300 64.02900 ymin,ymax (A): -10.98900 34.07100 zmin,zma (A): 0.2840000 49.46500 x,y,z range (A): 45.56600 45.06000 49.18100 scale (grids/A): 3.257355 object centre (A): 41.24600 11.54100 24.87450 number of atom coordinates read : 1797 total number of charged atoms : 1631 net assigned charge : 7.000008 assigned positive charge : 266.6172 centred at (gu) : 95.17921 92.97005 91.23015 assigned negative charge : -259.6174 centred at (gu) : 95.57980 94.92935 91.41079 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 155478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17090 grid for indexing accessible points = 1.400000 m= 81492 mr = 108740 m= 33556 mr = 66272 m= 8993 mr = 27026 m= 1818 mr = 6449 m= 295 mr = 1196 m= 22 mr = 192 m= 0 mr = 5 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 4083 time to turn everything in is 1.050000 number of dielectric boundary points 71774 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 13048 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) : 2.171570 object centre at (A) : 41.24600 11.54100 24.87450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2931415 -6.9026276E-02 midg,1,midg; midg,igrid,midg 0.4872093 -1.045696 1,midg,midg; igrid,midg,midg 0.1162956 0.6993394 gauss-seidel spectral radius is 0.9993193 estimated iterations to convergence 302 setup time was (sec) 1.280000 now iterating at: 03:21:44 rms-change max change #iterations 9.937266 312.1853 at 10iterations 5.999621 152.7199 at 20iterations 3.595859 82.32770 at 30iterations 2.139538 44.00782 at 40iterations 1.271068 24.45540 at 50iterations 0.7562342 13.76364 at 60iterations 0.4463811 8.584076 at 70iterations 0.2633269 5.074043 at 80iterations 0.1557945 3.015183 at 90iterations 9.1749415E-02 1.728369 at 100iterations 5.4114431E-02 1.034033 at 110iterations 3.1887766E-02 0.5536212 at 120iterations 1.8743427E-02 0.3192596 at 130iterations 1.1026264E-02 0.2219388 at 140iterations 6.4872317E-03 0.1217117 at 150iterations 3.8105021E-03 6.8349838E-02 at 160iterations 2.2403039E-03 3.9705276E-02 at 170iterations 1.3178515E-03 2.2998571E-02 at 180iterations finished qdiffx linear iterations at : 03:21:55 total time elapsed so far: 12.65000 # loops : 180 mean,max change (kT/e) : 1.3178515E-03 2.2998571E-02 energy calculations done at 12.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.78000 DelPhi exited at 03:21:56 12.786u 0.211s 0:13.43 96.7% 0+0k 0+0io 0pf+0w