Tue Oct 11 03:19:19 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+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 03:19:19 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3576 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: 0.5075201 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): -37.43800 23.73700 ymin,ymax (A): -33.98400 24.41900 zmin,zma (A): -23.99200 46.15300 x,y,z range (A): 61.17500 58.40300 70.14500 scale (grids/A): 0.5075201 object centre (A): -6.850500 -4.782500 11.08050 number of atom coordinates read : 3576 total number of charged atoms : 3415 net assigned charge : -5.999980 assigned positive charge : 531.4440 centred at (gu) : 91.22281 92.76407 88.94205 assigned negative charge : -537.4459 centred at (gu) : 91.20636 92.71206 89.02200 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6120 nv = 96 ne = 84 npr = 66778 no. pairs analyzed = 66778 no. exposed pairs = 5560 no. arc points = 39907 no. surface atoms = 1830 nbur = 1746 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 = 1.680000 m= 240 mr = 2588 m= 0 mr = 1 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3768 ## 565 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8161 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5312048E-11 -1.6204685E-10 midg,1,midg; midg,igrid,midg -8.1062643E-11 2.5001355E-11 1,midg,midg; igrid,midg,midg -7.6926056E-11 -6.8313112E-11 gauss-seidel spectral radius is 0.9800877 estimated iterations to convergence 59 setup time was (sec) 0.4300000 now iterating at: 03:19:19 rms-change max change #iterations 5.3860515E-02 9.482025 at 10iterations 3.0477745E-03 0.4837608 at 20iterations 2.5087787E-04 5.5458069E-02 at 30iterations 4.4136668E-05 1.1716843E-02 at 40iterations 9.7340953E-06 2.5768280E-03 at 50iterations finished qdiffx linear iterations at : 03:19:22 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 9.7340953E-06 2.5768280E-03 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 03:19:23 3.520u 0.187s 0:04.05 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 03:19:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3576 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: 1.522560 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): -37.43800 23.73700 ymin,ymax (A): -33.98400 24.41900 zmin,zma (A): -23.99200 46.15300 x,y,z range (A): 61.17500 58.40300 70.14500 scale (grids/A): 1.522560 object centre (A): -6.850500 -4.782500 11.08050 number of atom coordinates read : 3576 total number of charged atoms : 3415 net assigned charge : -5.999980 assigned positive charge : 531.4440 centred at (gu) : 93.66769 98.29115 86.82458 assigned negative charge : -537.4459 centred at (gu) : 93.61861 98.13586 87.06546 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 67933 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39907 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 17688 mr = 40749 m= 1388 mr = 10524 m= 29 mr = 438 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 113 time to turn everything in is 0.3400000 number of dielectric boundary points 35327 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 452 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 25650 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) : 0.5075201 object centre at (A) : -6.850500 -4.782500 11.08050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4806541E-02 -1.8125119E-02 midg,1,midg; midg,igrid,midg -5.6876852E-03 -6.0117524E-03 1,midg,midg; igrid,midg,midg -5.1103281E-03 -5.9633972E-03 gauss-seidel spectral radius is 0.9979897 estimated iterations to convergence 177 setup time was (sec) 0.5600000 now iterating at: 03:19:24 rms-change max change #iterations 3.141457 189.8412 at 10iterations 1.241422 48.19534 at 20iterations 0.4923341 19.34746 at 30iterations 0.1950848 8.444316 at 40iterations 7.7208288E-02 3.158885 at 50iterations 3.0666402E-02 1.228523 at 60iterations 1.2198074E-02 0.4519463 at 70iterations 4.8494497E-03 0.1967869 at 80iterations 1.9316421E-03 8.9874268E-02 at 90iterations 7.7826757E-04 2.8770447E-02 at 100iterations 3.1447562E-04 1.1642456E-02 at 110iterations 1.2989095E-04 4.8027039E-03 at 120iterations finished qdiffx linear iterations at : 03:19:31 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 1.2989095E-04 4.8027039E-03 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 03:19:31 7.909u 0.215s 0:08.57 94.6% 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 03:19:32 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 = 3576 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: 2.283841 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): -37.43800 23.73700 ymin,ymax (A): -33.98400 24.41900 zmin,zma (A): -23.99200 46.15300 x,y,z range (A): 61.17500 58.40300 70.14500 scale (grids/A): 2.283841 object centre (A): -6.850500 -4.782500 11.08050 number of atom coordinates read : 3576 total number of charged atoms : 3415 net assigned charge : -5.999980 assigned positive charge : 531.4440 centred at (gu) : 95.50127 102.4366 85.23658 assigned negative charge : -537.4459 centred at (gu) : 95.42779 102.2039 85.59803 start vw surface at 0.1100000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 157617 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39907 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 63418 mr = 101268 m= 15078 mr = 45998 m= 1728 mr = 10042 m= 78 mr = 849 m= 0 mr = 8 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 376 time to turn everything in is 0.8100000 number of dielectric boundary points 79754 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 49 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 27218 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) : 1.522560 object centre at (A) : -6.850500 -4.782500 11.08050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1877306 -0.3643848 midg,1,midg; midg,igrid,midg -9.8822966E-02 -7.0099853E-02 1,midg,midg; igrid,midg,midg -8.6328179E-02 -6.6132233E-02 gauss-seidel spectral radius is 0.9990955 estimated iterations to convergence 263 setup time was (sec) 1.050000 now iterating at: 03:19:33 rms-change max change #iterations 8.704685 329.4312 at 10iterations 4.908974 147.2742 at 20iterations 2.744103 76.74478 at 30iterations 1.525759 40.03068 at 40iterations 0.8408603 19.89454 at 50iterations 0.4610868 11.17369 at 60iterations 0.2527262 5.649267 at 70iterations 0.1380626 3.141029 at 80iterations 7.5427763E-02 1.796671 at 90iterations 4.1055724E-02 0.9080505 at 100iterations 2.2333330E-02 0.4720421 at 110iterations 1.2096359E-02 0.2579365 at 120iterations 6.5824846E-03 0.1381092 at 130iterations 3.5596732E-03 7.3619843E-02 at 140iterations 1.9384386E-03 4.1765213E-02 at 150iterations 1.0533576E-03 2.1222830E-02 at 160iterations 5.7362462E-04 1.2240887E-02 at 170iterations 3.1215884E-04 7.4768066E-03 at 180iterations finished qdiffx linear iterations at : 03:19:45 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 3.1215884E-04 7.4768066E-03 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 03:19:45 12.877u 0.234s 0:13.57 96.5% 0+0k 0+0io 0pf+0w