Tue Oct 11 06:45:49 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 06:45:49 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 = 2345 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: 0.6832489 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): -13.79800 38.30600 ymin,ymax (A): 44.95200 96.09900 zmin,zma (A): -4.732000 40.97800 x,y,z range (A): 52.10400 51.14700 45.71000 scale (grids/A): 0.6832489 object centre (A): 12.25400 70.52550 18.12300 number of atom coordinates read : 2345 total number of charged atoms : 2217 net assigned charge : 11.50001 assigned positive charge : 358.2986 centred at (gu) : 89.58415 88.56309 90.01870 assigned negative charge : -346.7990 centred at (gu) : 89.57916 88.42785 89.90331 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7264 nv = 96 ne = 84 npr = 47511 no. pairs analyzed = 47511 no. exposed pairs = 2847 no. arc points = 19516 no. surface atoms = 974 nbur = 1371 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 464 mr = 4128 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3544 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1935 ## 168 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8464 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7657921E-08 9.0428394E-08 midg,1,midg; midg,igrid,midg 1.4014009E-08 7.2392730E-08 1,midg,midg; igrid,midg,midg 5.7211540E-08 5.1562246E-08 gauss-seidel spectral radius is 0.9888643 estimated iterations to convergence 77 setup time was (sec) 0.6100000 now iterating at: 06:45:50 rms-change max change #iterations 0.1834292 24.00095 at 10iterations 2.1032697E-02 3.492996 at 20iterations 2.4839286E-03 0.3155007 at 30iterations 3.2170754E-04 5.3653717E-02 at 40iterations 6.0977138E-05 8.1119537E-03 at 50iterations finished qdiffx linear iterations at : 06:45:54 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 6.0977138E-05 8.1119537E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 06:45:54 4.182u 0.283s 0:05.70 78.2% 0+0k 0+0io 5pf+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 06:45:54 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 = 2345 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: 2.049747 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): -13.79800 38.30600 ymin,ymax (A): 44.95200 96.09900 zmin,zma (A): -4.732000 40.97800 x,y,z range (A): 52.10400 51.14700 45.71000 scale (grids/A): 2.049747 object centre (A): 12.25400 70.52550 18.12300 number of atom coordinates read : 2345 total number of charged atoms : 2217 net assigned charge : 11.50001 assigned positive charge : 358.2986 centred at (gu) : 88.75230 85.68909 90.05573 assigned negative charge : -346.7990 centred at (gu) : 88.73745 85.28361 89.70988 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 77570 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19516 grid for indexing accessible points = 1.400000 m= 30138 mr = 54722 m= 5521 mr = 22399 m= 416 mr = 3547 m= 8 mr = 175 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 32810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 123 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 17554 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) : 0.6832489 object centre at (A) : 12.25400 70.52550 18.12300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4409296E-03 4.4568915E-02 midg,1,midg; midg,igrid,midg 4.4556212E-02 5.4904509E-02 1,midg,midg; igrid,midg,midg 8.8575728E-02 5.0484631E-02 gauss-seidel spectral radius is 0.9987830 estimated iterations to convergence 227 setup time was (sec) 1.050000 now iterating at: 06:45:56 rms-change max change #iterations 4.610777 174.8088 at 10iterations 2.261633 76.26891 at 20iterations 1.101433 33.99799 at 30iterations 0.5407431 16.52353 at 40iterations 0.2647676 9.000214 at 50iterations 0.1298356 3.621631 at 60iterations 6.3279346E-02 1.938478 at 70iterations 3.0988963E-02 1.019201 at 80iterations 1.5188707E-02 0.4972382 at 90iterations 7.4596894E-03 0.2164879 at 100iterations 3.6513868E-03 0.1124034 at 110iterations 1.8005566E-03 5.0342560E-02 at 120iterations finished qdiffx linear iterations at : 06:46:04 total time elapsed so far: 9.720000 # loops : 120 mean,max change (kT/e) : 1.8005566E-03 5.0342560E-02 energy calculations done at 9.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.900000 DelPhi exited at 06:46:05 9.903u 0.312s 0:10.67 95.6% 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 06:46:05 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 = 2345 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: 3.074620 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): -13.79800 38.30600 ymin,ymax (A): 44.95200 96.09900 zmin,zma (A): -4.732000 40.97800 x,y,z range (A): 52.10400 51.14700 45.71000 scale (grids/A): 3.074620 object centre (A): 12.25400 70.52550 18.12300 number of atom coordinates read : 2345 total number of charged atoms : 2217 net assigned charge : 11.50001 assigned positive charge : 358.2986 centred at (gu) : 88.12830 83.53367 90.08358 assigned negative charge : -346.7990 centred at (gu) : 88.10610 82.92536 89.56490 start vw surface at 0.1500000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 179043 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19516 grid for indexing accessible points = 1.400000 m= 94793 mr = 131988 m= 37167 mr = 78262 m= 10231 mr = 29908 m= 1846 mr = 7725 m= 147 mr = 1346 m= 0 mr = 43 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.890000 number of dielectric boundary points 73955 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 17736 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) : 2.049747 object centre at (A) : 12.25400 70.52550 18.12300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.5831589E-02 0.4682024 midg,1,midg; midg,igrid,midg 0.3481722 0.5345823 1,midg,midg; igrid,midg,midg 1.187824 0.5872260 gauss-seidel spectral radius is 0.9992902 estimated iterations to convergence 296 setup time was (sec) 2.220000 now iterating at: 06:46:08 rms-change max change #iterations 10.53750 432.8277 at 10iterations 6.259230 198.5400 at 20iterations 3.700235 79.44113 at 30iterations 2.186116 42.47901 at 40iterations 1.285095 25.58720 at 50iterations 0.7541721 14.34812 at 60iterations 0.4420677 7.644246 at 70iterations 0.2588508 4.977610 at 80iterations 0.1513652 2.857803 at 90iterations 8.8533536E-02 1.507341 at 100iterations 5.1836267E-02 0.8828852 at 110iterations 3.0290486E-02 0.5038300 at 120iterations 1.7772460E-02 0.3087330 at 130iterations 1.0438555E-02 0.1897049 at 140iterations 6.1842054E-03 0.1162949 at 150iterations 3.7262507E-03 7.9116821E-02 at 160iterations 2.3029498E-03 4.0734291E-02 at 170iterations 1.4827998E-03 2.8953552E-02 at 180iterations finished qdiffx linear iterations at : 06:46:22 total time elapsed so far: 16.36000 # loops : 180 mean,max change (kT/e) : 1.4827998E-03 2.8953552E-02 energy calculations done at 16.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.54000 DelPhi exited at 06:46:22 16.540u 0.351s 0:17.34 97.4% 0+0k 0+0io 0pf+0w