Tue Oct 11 03:16:40 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 03:16:40 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 = 3732 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5607712 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): 20.93300 76.94600 ymin,ymax (A): 40.51800 104.0020 zmin,zma (A): 67.21000 126.9490 x,y,z range (A): 56.01300 63.48400 59.73901 scale (grids/A): 0.5607712 object centre (A): 48.93950 72.25999 97.07950 number of atom coordinates read : 3732 total number of charged atoms : 3602 net assigned charge : -6.999970 assigned positive charge : 571.5550 centred at (gu) : 88.57750 90.87704 89.58701 assigned negative charge : -578.5575 centred at (gu) : 88.56597 90.80930 89.57965 start vw surface at 0.2000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7905 nv = 96 ne = 84 npr = 70501 no. pairs analyzed = 70501 no. exposed pairs = 5473 no. arc points = 39835 no. surface atoms = 1792 nbur = 1940 mkacc time = 0.1600000 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 = 1.540000 m= 355 mr = 3605 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 4645 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3892 ## 408 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 10082 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.6928299E-10 -6.0124528E-10 midg,1,midg; midg,igrid,midg -1.4425933E-09 2.8607483E-10 1,midg,midg; igrid,midg,midg -1.3206098E-09 -4.3335380E-10 gauss-seidel spectral radius is 0.9836796 estimated iterations to convergence 64 setup time was (sec) 0.6200000 now iterating at: 03:16:40 rms-change max change #iterations 8.9911535E-02 14.34292 at 10iterations 6.3493340E-03 0.8947334 at 20iterations 4.6538512E-04 6.3988484E-02 at 30iterations 4.0370680E-05 5.2034855E-03 at 40iterations 6.5929335E-06 7.7438354E-04 at 50iterations finished qdiffx linear iterations at : 03:16:43 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 6.5929335E-06 7.7438354E-04 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 03:16:44 3.490u 0.207s 0:04.04 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 03:16:44 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 = 3732 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.682314 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): 20.93300 76.94600 ymin,ymax (A): 40.51800 104.0020 zmin,zma (A): 67.21000 126.9490 x,y,z range (A): 56.01300 63.48400 59.73901 scale (grids/A): 1.682314 object centre (A): 48.93950 72.25999 97.07950 number of atom coordinates read : 3732 total number of charged atoms : 3602 net assigned charge : -6.999970 assigned positive charge : 571.5550 centred at (gu) : 85.73110 92.63015 88.75967 assigned negative charge : -578.5575 centred at (gu) : 85.69758 92.42757 88.73859 start vw surface at 0.2300000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 85577 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39835 grid for indexing accessible points = 1.400000 m= 27305 mr = 53583 m= 3279 mr = 17925 m= 110 mr = 1567 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 115 time to turn everything in is 0.6700000 number of dielectric boundary points 43192 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 317 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 27741 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) : 0.5607712 object centre at (A) : 48.93950 72.25999 97.07950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.6775509E-03 2.5649290E-03 midg,1,midg; midg,igrid,midg -2.5543394E-02 9.1764424E-03 1,midg,midg; igrid,midg,midg -1.6780041E-02 4.7286032E-03 gauss-seidel spectral radius is 0.9984115 estimated iterations to convergence 199 setup time was (sec) 0.9600000 now iterating at: 03:16:45 rms-change max change #iterations 4.181183 168.3566 at 10iterations 1.831899 69.20383 at 20iterations 0.8033133 27.43849 at 30iterations 0.3517770 10.75905 at 40iterations 0.1552359 5.036581 at 50iterations 6.8473265E-02 2.284837 at 60iterations 3.0111058E-02 0.9802575 at 70iterations 1.3250729E-02 0.4526882 at 80iterations 5.8381367E-03 0.1843491 at 90iterations 2.5765134E-03 8.9691162E-02 at 100iterations 1.1402657E-03 3.3120632E-02 at 110iterations 5.0286320E-04 1.5550613E-02 at 120iterations finished qdiffx linear iterations at : 03:16:51 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 5.0286320E-04 1.5550613E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 03:16:52 7.737u 0.157s 0:08.20 96.0% 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 03:16:52 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 = 3732 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.523470 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): 20.93300 76.94600 ymin,ymax (A): 40.51800 104.0020 zmin,zma (A): 67.21000 126.9490 x,y,z range (A): 56.01300 63.48400 59.73901 scale (grids/A): 2.523470 object centre (A): 48.93950 72.25999 97.07950 number of atom coordinates read : 3732 total number of charged atoms : 3602 net assigned charge : -6.999970 assigned positive charge : 571.5550 centred at (gu) : 83.59641 93.94455 88.13900 assigned negative charge : -578.5575 centred at (gu) : 83.54636 93.64143 88.10760 start vw surface at 0.1800000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 197781 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39835 grid for indexing accessible points = 1.400000 m= 90392 mr = 131941 m= 28794 mr = 68381 m= 5249 mr = 21291 m= 393 mr = 3412 m= 11 mr = 156 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 421 time to turn everything in is 1.530000 number of dielectric boundary points 97439 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 28803 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) : 1.682314 object centre at (A) : 48.93950 72.25999 97.07950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.3747638E-02 6.3951761E-02 midg,1,midg; midg,igrid,midg -0.3784998 0.2412242 1,midg,midg; igrid,midg,midg -0.2274304 6.7420170E-02 gauss-seidel spectral radius is 0.9992539 estimated iterations to convergence 289 setup time was (sec) 1.840000 now iterating at: 03:16:54 rms-change max change #iterations 10.98104 376.6658 at 10iterations 6.528876 226.2745 at 20iterations 3.869030 87.68610 at 30iterations 2.273330 54.85516 at 40iterations 1.326761 31.07062 at 50iterations 0.7735986 17.62954 at 60iterations 0.4488752 9.667118 at 70iterations 0.2601614 5.699603 at 80iterations 0.1504661 2.561218 at 90iterations 8.6969607E-02 1.601077 at 100iterations 5.0063673E-02 0.9362669 at 110iterations 2.8857201E-02 0.5546532 at 120iterations 1.6611051E-02 0.3075390 at 130iterations 9.5337350E-03 0.1975093 at 140iterations 5.4887207E-03 0.1010265 at 150iterations 3.1479886E-03 5.9288621E-02 at 160iterations 1.8058129E-03 3.2812119E-02 at 170iterations 1.0379355E-03 1.8186569E-02 at 180iterations finished qdiffx linear iterations at : 03:17:06 total time elapsed so far: 13.73000 # loops : 180 mean,max change (kT/e) : 1.0379355E-03 1.8186569E-02 energy calculations done at 13.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.93000 DelPhi exited at 03:17:07 13.935u 0.227s 0:14.73 96.0% 0+0k 0+0io 0pf+0w