Sun Oct 9 09:07:19 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 Sun Oct 9 2011 at 09:07:19 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2800 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: 0.5421375 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): -8.963000 49.20000 ymin,ymax (A): 14.48700 66.51900 zmin,zma (A): 5.076000 70.74200 x,y,z range (A): 58.16300 52.03200 65.66600 scale (grids/A): 0.5421375 object centre (A): 20.11850 40.50300 37.90900 number of atom coordinates read : 2800 total number of charged atoms : 2656 net assigned charge : 2.000030 assigned positive charge : 413.2975 centred at (gu) : 89.31596 90.55391 90.09297 assigned negative charge : -411.2983 centred at (gu) : 89.34978 90.63497 89.95992 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5404 nv = 96 ne = 84 npr = 56253 no. pairs analyzed = 56253 no. exposed pairs = 3541 no. arc points = 25455 no. surface atoms = 1197 nbur = 1603 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 217 mr = 2729 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2886 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2611 ## 331 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7060 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.9718941E-10 8.2332330E-10 midg,1,midg; midg,igrid,midg 4.6583504E-10 -3.7773529E-10 1,midg,midg; igrid,midg,midg 3.4111536E-10 -6.0218185E-11 gauss-seidel spectral radius is 0.9824525 estimated iterations to convergence 62 setup time was (sec) 0.5400000 now iterating at: 09:07:20 rms-change max change #iterations 6.7937464E-02 15.17497 at 10iterations 4.3782778E-03 0.7789001 at 20iterations 2.9289536E-04 5.6023598E-02 at 30iterations 1.9432875E-05 3.5772324E-03 at 40iterations 1.4279655E-06 2.2983551E-04 at 50iterations finished qdiffx linear iterations at : 09:07:23 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.4279655E-06 2.2983551E-04 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 09:07:23 3.459u 0.207s 0:03.95 92.4% 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 Sun Oct 9 2011 at 09:07:23 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2800 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: 1.626412 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): -8.963000 49.20000 ymin,ymax (A): 14.48700 66.51900 zmin,zma (A): 5.076000 70.74200 x,y,z range (A): 58.16300 52.03200 65.66600 scale (grids/A): 1.626412 object centre (A): 20.11850 40.50300 37.90900 number of atom coordinates read : 2800 total number of charged atoms : 2656 net assigned charge : 2.000030 assigned positive charge : 413.2975 centred at (gu) : 87.94726 91.66127 90.27827 assigned negative charge : -411.2983 centred at (gu) : 88.04912 91.90475 89.87931 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 59570 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25455 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18193 mr = 39767 m= 1841 mr = 12422 m= 53 mr = 810 m= 0 mr = 3 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 67 time to turn everything in is 0.4600000 number of dielectric boundary points 26655 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 317 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 20348 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) : 0.5421375 object centre at (A) : 20.11850 40.50300 37.90900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2446227E-02 1.2968212E-02 midg,1,midg; midg,igrid,midg 6.9641159E-03 -4.6848897E-03 1,midg,midg; igrid,midg,midg -8.7516499E-04 -5.8350964E-03 gauss-seidel spectral radius is 0.9981589 estimated iterations to convergence 185 setup time was (sec) 0.7400000 now iterating at: 09:07:24 rms-change max change #iterations 3.146461 197.2106 at 10iterations 1.293425 54.37555 at 20iterations 0.5354242 20.27102 at 30iterations 0.2208340 9.631857 at 40iterations 9.1696657E-02 3.696316 at 50iterations 3.8040321E-02 1.490274 at 60iterations 1.5701866E-02 0.5726974 at 70iterations 6.5357671E-03 0.2389784 at 80iterations 2.7032318E-03 0.1070881 at 90iterations 1.1238069E-03 4.5326233E-02 at 100iterations 4.6521489E-04 1.7031193E-02 at 110iterations 1.9310784E-04 8.1100464E-03 at 120iterations finished qdiffx linear iterations at : 09:07:31 total time elapsed so far: 7.160000 # loops : 120 mean,max change (kT/e) : 1.9310784E-04 8.1100464E-03 energy calculations done at 7.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.340000 DelPhi exited at 09:07:31 7.346u 0.229s 0:07.84 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 Sun Oct 9 2011 at 09:07:31 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2800 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: 2.439619 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): -8.963000 49.20000 ymin,ymax (A): 14.48700 66.51900 zmin,zma (A): 5.076000 70.74200 x,y,z range (A): 58.16300 52.03200 65.66600 scale (grids/A): 2.439619 object centre (A): 20.11850 40.50300 37.90900 number of atom coordinates read : 2800 total number of charged atoms : 2656 net assigned charge : 2.000030 assigned positive charge : 413.2975 centred at (gu) : 86.92048 92.49185 90.41724 assigned negative charge : -411.2983 centred at (gu) : 87.07364 92.85697 89.81891 start vw surface at 0.1400000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 138348 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25455 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 62762 mr = 97401 m= 17861 mr = 49513 m= 2784 mr = 13212 m= 175 mr = 1624 m= 2 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 217 time to turn everything in is 1.050000 number of dielectric boundary points 60113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 21224 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) : 1.626412 object centre at (A) : 20.11850 40.50300 37.90900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2730143 0.1399896 midg,1,midg; midg,igrid,midg 0.1045454 -8.8287115E-02 1,midg,midg; igrid,midg,midg -5.1266499E-02 -0.1506083 gauss-seidel spectral radius is 0.9991264 estimated iterations to convergence 267 setup time was (sec) 1.370000 now iterating at: 09:07:33 rms-change max change #iterations 8.284721 271.4206 at 10iterations 4.641320 123.1151 at 20iterations 2.589583 75.61523 at 30iterations 1.435313 31.76202 at 40iterations 0.7927163 18.21219 at 50iterations 0.4385807 10.82623 at 60iterations 0.2403934 5.464424 at 70iterations 0.1325654 3.111809 at 80iterations 7.2576500E-02 1.781097 at 90iterations 3.9822701E-02 0.8323650 at 100iterations 2.1803524E-02 0.4845905 at 110iterations 1.1978147E-02 0.2573986 at 120iterations 6.5650488E-03 0.1443200 at 130iterations 3.5923221E-03 7.5284958E-02 at 140iterations 1.9674506E-03 4.3422699E-02 at 150iterations 1.0747497E-03 2.3592591E-02 at 160iterations 5.8895600E-04 1.3244629E-02 at 170iterations 3.2214762E-04 7.5595379E-03 at 180iterations finished qdiffx linear iterations at : 09:07:43 total time elapsed so far: 11.56000 # loops : 180 mean,max change (kT/e) : 3.2214762E-04 7.5595379E-03 energy calculations done at 11.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.73000 DelPhi exited at 09:07:43 11.732u 0.241s 0:12.24 97.7% 0+0k 0+0io 0pf+0w