Sun Oct 9 01:57:53 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 01:57:53 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2434 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6323156 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): 13.79100 67.68000 ymin,ymax (A): -30.66300 25.63800 zmin,zma (A): 2.448000 46.11300 x,y,z range (A): 53.88900 56.30100 43.66500 scale (grids/A): 0.6323156 object centre (A): 40.73550 -2.512500 24.28050 number of atom coordinates read : 2434 total number of charged atoms : 2299 net assigned charge : 11.51402 assigned positive charge : 359.2961 centred at (gu) : 90.08693 90.67863 89.49278 assigned negative charge : -347.7830 centred at (gu) : 90.12630 90.69152 89.58922 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6903 nv = 96 ne = 84 npr = 47370 no. pairs analyzed = 47370 no. exposed pairs = 3273 no. arc points = 23441 no. surface atoms = 1094 nbur = 1340 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 422 mr = 3626 m= 4 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3660 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2373 ## 223 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8092 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3899743E-08 4.6607425E-09 midg,1,midg; midg,igrid,midg 1.2550272E-08 1.4148766E-08 1,midg,midg; igrid,midg,midg 1.6384938E-08 1.0208805E-08 gauss-seidel spectral radius is 0.9870439 estimated iterations to convergence 72 setup time was (sec) 0.3700000 now iterating at: 01:57:53 rms-change max change #iterations 0.1351392 20.68104 at 10iterations 1.3026301E-02 1.951908 at 20iterations 1.6162867E-03 0.2445679 at 30iterations 4.0342871E-04 6.7770004E-02 at 40iterations 1.4319921E-04 2.4562836E-02 at 50iterations finished qdiffx linear iterations at : 01:57:56 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.4319921E-04 2.4562836E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 01:57:57 3.334u 0.178s 0:03.80 92.1% 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 Sun Oct 9 2011 at 01:57:57 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2434 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.896947 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): 13.79100 67.68000 ymin,ymax (A): -30.66300 25.63800 zmin,zma (A): 2.448000 46.11300 x,y,z range (A): 53.88900 56.30100 43.66500 scale (grids/A): 1.896947 object centre (A): 40.73550 -2.512500 24.28050 number of atom coordinates read : 2434 total number of charged atoms : 2299 net assigned charge : 11.51402 assigned positive charge : 359.2961 centred at (gu) : 90.26038 92.03543 88.47787 assigned negative charge : -347.7830 centred at (gu) : 90.37880 92.07427 88.76765 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 73977 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23441 grid for indexing accessible points = 1.400000 m= 27533 mr = 49983 m= 4765 mr = 19736 m= 326 mr = 2961 m= 2 mr = 109 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 0.3500000 number of dielectric boundary points 33814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 18122 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) : 0.6323156 object centre at (A) : 40.73550 -2.512500 24.28050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7773613E-02 -1.1583415E-03 midg,1,midg; midg,igrid,midg 5.1235683E-02 2.9508250E-02 1,midg,midg; igrid,midg,midg 5.7961445E-02 4.5588832E-02 gauss-seidel spectral radius is 0.9986275 estimated iterations to convergence 214 setup time was (sec) 0.5700000 now iterating at: 01:57:57 rms-change max change #iterations 4.003096 169.8862 at 10iterations 1.862242 64.77634 at 20iterations 0.8708482 27.79050 at 30iterations 0.4058840 13.38449 at 40iterations 0.1890520 5.773041 at 50iterations 8.8449888E-02 2.792149 at 60iterations 4.1456651E-02 1.332568 at 70iterations 1.9378629E-02 0.6933632 at 80iterations 9.1444552E-03 0.2863684 at 90iterations 4.3885233E-03 0.1491241 at 100iterations 2.1674102E-03 7.3204041E-02 at 110iterations 1.1217477E-03 4.0237427E-02 at 120iterations finished qdiffx linear iterations at : 01:58:05 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 1.1217477E-03 4.0237427E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 01:58:05 7.859u 0.201s 0:08.38 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 Sun Oct 9 2011 at 01:58:05 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2434 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.845420 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): 13.79100 67.68000 ymin,ymax (A): -30.66300 25.63800 zmin,zma (A): 2.448000 46.11300 x,y,z range (A): 53.88900 56.30100 43.66500 scale (grids/A): 2.845420 object centre (A): 40.73550 -2.512500 24.28050 number of atom coordinates read : 2434 total number of charged atoms : 2299 net assigned charge : 11.51402 assigned positive charge : 359.2961 centred at (gu) : 90.39052 93.05297 87.71675 assigned negative charge : -347.7830 centred at (gu) : 90.56827 93.11140 88.15144 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 170562 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23441 grid for indexing accessible points = 1.400000 m= 86926 mr = 120982 m= 33169 mr = 70070 m= 8664 mr = 26221 m= 1329 mr = 6378 m= 78 mr = 836 m= 0 mr = 21 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9300000 number of dielectric boundary points 76220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 18390 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) : 1.896947 object centre at (A) : 40.73550 -2.512500 24.28050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2878021 -3.1724472E-02 midg,1,midg; midg,igrid,midg 0.7187673 0.3538813 1,midg,midg; igrid,midg,midg 0.6831407 0.4902118 gauss-seidel spectral radius is 0.9992651 estimated iterations to convergence 291 setup time was (sec) 1.180000 now iterating at: 01:58:06 rms-change max change #iterations 9.568373 457.6606 at 10iterations 5.647666 132.3441 at 20iterations 3.300194 75.31013 at 30iterations 1.926155 58.93364 at 40iterations 1.119256 22.42762 at 50iterations 0.6501729 12.06853 at 60iterations 0.3770891 8.646700 at 70iterations 0.2185912 4.948061 at 80iterations 0.1262609 2.537815 at 90iterations 7.2968364E-02 1.396108 at 100iterations 4.2267665E-02 0.8134508 at 110iterations 2.4375470E-02 0.4384651 at 120iterations 1.4101414E-02 0.2819862 at 130iterations 8.1609432E-03 0.1607170 at 140iterations 4.7494774E-03 9.3458176E-02 at 150iterations 2.7790901E-03 5.5313110E-02 at 160iterations 1.6550611E-03 4.2127609E-02 at 170iterations 1.0122507E-03 2.2550583E-02 at 180iterations finished qdiffx linear iterations at : 01:58:18 total time elapsed so far: 12.61000 # loops : 180 mean,max change (kT/e) : 1.0122507E-03 2.2550583E-02 energy calculations done at 12.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.74000 DelPhi exited at 01:58:18 12.741u 0.226s 0:13.24 97.8% 0+0k 0+0io 0pf+0w