Sat Oct 8 17:27:18 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 Sat Oct 8 2011 at 17:27:18 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3741 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5541633 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): -1.893000 60.24400 ymin,ymax (A): -18.44900 44.40100 zmin,zma (A): -5.310000 58.93100 x,y,z range (A): 62.13700 62.85000 64.24100 scale (grids/A): 0.5541633 object centre (A): 29.17550 12.97600 26.81050 number of atom coordinates read : 3741 total number of charged atoms : 3590 net assigned charge : -9.999960 assigned positive charge : 569.9274 centred at (gu) : 88.88784 86.66348 90.40226 assigned negative charge : -579.9298 centred at (gu) : 88.96622 86.68796 90.43293 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7514 nv = 96 ne = 84 npr = 75766 no. pairs analyzed = 75766 no. exposed pairs = 4834 no. arc points = 33913 no. surface atoms = 1612 nbur = 2129 mkacc time = 0.2000000 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= 313 mr = 3902 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 3918 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3378 ## 406 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 9788 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6339327E-10 -1.3390925E-09 midg,1,midg; midg,igrid,midg -1.2708820E-09 -5.2203358E-10 1,midg,midg; igrid,midg,midg 6.0477283E-11 -1.3560540E-09 gauss-seidel spectral radius is 0.9832661 estimated iterations to convergence 64 setup time was (sec) 0.7700000 now iterating at: 17:27:19 rms-change max change #iterations 9.1033086E-02 15.07906 at 10iterations 6.5050395E-03 0.9483871 at 20iterations 5.5999780E-04 7.8607559E-02 at 30iterations 1.0414398E-04 1.8963814E-02 at 40iterations 2.9603812E-05 5.2738190E-03 at 50iterations finished qdiffx linear iterations at : 17:27:24 total time elapsed so far: 5.190000 # loops : 50 mean,max change (kT/e) : 2.9603812E-05 5.2738190E-03 energy calculations done at 5.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.360000 DelPhi exited at 17:27:24 5.363u 0.452s 0:06.22 93.4% 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 Sat Oct 8 2011 at 17:27:25 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3741 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.662490 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): -1.893000 60.24400 ymin,ymax (A): -18.44900 44.40100 zmin,zma (A): -5.310000 58.93100 x,y,z range (A): 62.13700 62.85000 64.24100 scale (grids/A): 1.662490 object centre (A): 29.17550 12.97600 26.81050 number of atom coordinates read : 3741 total number of charged atoms : 3590 net assigned charge : -9.999960 assigned positive charge : 569.9274 centred at (gu) : 86.66241 79.98929 91.20586 assigned negative charge : -579.9298 centred at (gu) : 86.89819 80.06323 91.29845 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 82950 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33913 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 26035 mr = 56500 m= 2728 mr = 17603 m= 81 mr = 1218 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.7200000 number of dielectric boundary points 36469 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 351 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 27595 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) : 0.5541633 object centre at (A) : 29.17550 12.97600 26.81050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3710418E-03 -1.2017110E-02 midg,1,midg; midg,igrid,midg -2.8728485E-02 -9.3862070E-03 1,midg,midg; igrid,midg,midg -1.2538539E-02 -3.5392009E-02 gauss-seidel spectral radius is 0.9983212 estimated iterations to convergence 194 setup time was (sec) 1.130000 now iterating at: 17:27:26 rms-change max change #iterations 4.029084 161.7329 at 10iterations 1.730170 61.45400 at 20iterations 0.7491274 32.69423 at 30iterations 0.3227544 10.54195 at 40iterations 0.1391345 4.907935 at 50iterations 5.9911072E-02 1.847644 at 60iterations 2.5846528E-02 0.7778077 at 70iterations 1.1222626E-02 0.3427963 at 80iterations 4.8452434E-03 0.1723557 at 90iterations 2.1051688E-03 6.6968918E-02 at 100iterations 9.2881988E-04 2.9472351E-02 at 110iterations 4.1908716E-04 1.3400078E-02 at 120iterations finished qdiffx linear iterations at : 17:27:38 total time elapsed so far: 13.28000 # loops : 120 mean,max change (kT/e) : 4.1908716E-04 1.3400078E-02 energy calculations done at 13.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.45000 DelPhi exited at 17:27:39 13.453u 0.532s 0:14.25 98.1% 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 Sat Oct 8 2011 at 17:27:39 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3741 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.493735 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): -1.893000 60.24400 ymin,ymax (A): -18.44900 44.40100 zmin,zma (A): -5.310000 58.93100 x,y,z range (A): 62.13700 62.85000 64.24100 scale (grids/A): 2.493735 object centre (A): 29.17550 12.97600 26.81050 number of atom coordinates read : 3741 total number of charged atoms : 3590 net assigned charge : -9.999960 assigned positive charge : 569.9274 centred at (gu) : 84.99313 74.98360 91.80852 assigned negative charge : -579.9298 centred at (gu) : 85.34719 75.09470 91.94765 start vw surface at 0.1500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 192675 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33913 grid for indexing accessible points = 1.400000 m= 90009 mr = 138404 m= 25450 mr = 70662 m= 4178 mr = 18660 m= 306 mr = 2497 m= 7 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 1.770000 number of dielectric boundary points 82318 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 28692 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) : 1.662490 object centre at (A) : 29.17550 12.97600 26.81050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4617390E-02 2.3832541E-02 midg,1,midg; midg,igrid,midg -0.4327075 -0.1128297 1,midg,midg; igrid,midg,midg -0.2016635 -0.6415464 gauss-seidel spectral radius is 0.9991971 estimated iterations to convergence 279 setup time was (sec) 2.180000 now iterating at: 17:27:41 rms-change max change #iterations 10.30710 350.7861 at 10iterations 5.903219 129.1549 at 20iterations 3.367291 72.01546 at 30iterations 1.911319 40.46350 at 40iterations 1.082632 21.03640 at 50iterations 0.6114039 11.97903 at 60iterations 0.3447471 7.260180 at 70iterations 0.1942659 3.662118 at 80iterations 0.1094301 2.056201 at 90iterations 6.1451431E-02 1.142944 at 100iterations 3.4566194E-02 0.6363583 at 110iterations 1.9441560E-02 0.3467674 at 120iterations 1.0920020E-02 0.1949577 at 130iterations 6.1388854E-03 0.1259995 at 140iterations 3.4531308E-03 6.3242912E-02 at 150iterations 1.9489406E-03 3.7113190E-02 at 160iterations 1.1008823E-03 1.9744873E-02 at 170iterations 6.2357710E-04 1.2203217E-02 at 180iterations finished qdiffx linear iterations at : 17:28:01 total time elapsed so far: 21.61000 # loops : 180 mean,max change (kT/e) : 6.2357710E-04 1.2203217E-02 energy calculations done at 21.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.78000 DelPhi exited at 17:28:01 21.787u 0.546s 0:22.67 98.4% 0+0k 0+0io 0pf+0w