Sat Oct 8 11:33:42 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 Sat Oct 8 2011 at 11:33:42 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 = 2371 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: 0.6627448 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): -59.57500 -11.52700 ymin,ymax (A): 54.12400 102.2870 zmin,zma (A): 38.44100 92.15700 x,y,z range (A): 48.04800 48.16300 53.71600 scale (grids/A): 0.6627448 object centre (A): -35.55100 78.20551 65.29900 number of atom coordinates read : 2371 total number of charged atoms : 2224 net assigned charge : -0.9999918 assigned positive charge : 342.5781 centred at (gu) : 91.48866 90.45076 91.92305 assigned negative charge : -343.5786 centred at (gu) : 91.45113 90.36992 91.97386 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7240 nv = 96 ne = 84 npr = 47474 no. pairs analyzed = 47474 no. exposed pairs = 3067 no. arc points = 21681 no. surface atoms = 1045 nbur = 1326 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 390 mr = 3883 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3702 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2059 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8312 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4636921E-09 -1.8374154E-08 midg,1,midg; midg,igrid,midg -1.6303101E-08 1.3506739E-08 1,midg,midg; igrid,midg,midg -7.1576109E-09 5.9466503E-09 gauss-seidel spectral radius is 0.9881880 estimated iterations to convergence 75 setup time was (sec) 0.3900000 now iterating at: 11:33:43 rms-change max change #iterations 0.1577209 23.55454 at 10iterations 1.7272262E-02 2.563736 at 20iterations 1.8235527E-03 0.2299538 at 30iterations 1.9629263E-04 2.4944305E-02 at 40iterations 2.1412361E-05 2.8915405E-03 at 50iterations finished qdiffx linear iterations at : 11:33:46 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 2.1412361E-05 2.8915405E-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) 3.500000 DelPhi exited at 11:33:46 3.505u 0.202s 0:03.99 92.7% 0+0k 0+0io 6pf+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 11:33:46 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 = 2371 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: 1.988234 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): -59.57500 -11.52700 ymin,ymax (A): 54.12400 102.2870 zmin,zma (A): 38.44100 92.15700 x,y,z range (A): 48.04800 48.16300 53.71600 scale (grids/A): 1.988234 object centre (A): -35.55100 78.20551 65.29900 number of atom coordinates read : 2371 total number of charged atoms : 2224 net assigned charge : -0.9999918 assigned positive charge : 342.5781 centred at (gu) : 94.46545 91.35176 95.76863 assigned negative charge : -343.5786 centred at (gu) : 94.35312 91.10947 95.92146 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 78000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21681 grid for indexing accessible points = 1.400000 m= 27919 mr = 53344 m= 4498 mr = 20393 m= 288 mr = 2758 m= 2 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.3900000 number of dielectric boundary points 34100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 17572 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) : 0.6627448 object centre at (A) : -35.55100 78.20551 65.29900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7056256E-02 -1.2455384E-03 midg,1,midg; midg,igrid,midg -1.8849378E-02 -5.7474887E-03 1,midg,midg; igrid,midg,midg -9.7230598E-03 2.3026699E-02 gauss-seidel spectral radius is 0.9987242 estimated iterations to convergence 222 setup time was (sec) 0.6400000 now iterating at: 11:33:47 rms-change max change #iterations 4.288561 172.3135 at 10iterations 2.056897 75.35400 at 20iterations 0.9861824 29.61861 at 30iterations 0.4717400 13.89275 at 40iterations 0.2271761 6.752143 at 50iterations 0.1089799 3.330850 at 60iterations 5.2252244E-02 1.673779 at 70iterations 2.5128404E-02 0.7418594 at 80iterations 1.2061323E-02 0.3773174 at 90iterations 5.7783085E-03 0.1755371 at 100iterations 2.7744393E-03 8.1844091E-02 at 110iterations 1.3287461E-03 4.3291211E-02 at 120iterations finished qdiffx linear iterations at : 11:33:56 total time elapsed so far: 8.640000 # loops : 120 mean,max change (kT/e) : 1.3287461E-03 4.3291211E-02 energy calculations done at 8.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.770000 DelPhi exited at 11:33:57 8.773u 0.250s 0:10.88 82.9% 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 11:33:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2371 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: 2.982352 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): -59.57500 -11.52700 ymin,ymax (A): 54.12400 102.2870 zmin,zma (A): 38.44100 92.15700 x,y,z range (A): 48.04800 48.16300 53.71600 scale (grids/A): 2.982352 object centre (A): -35.55100 78.20551 65.29900 number of atom coordinates read : 2371 total number of charged atoms : 2224 net assigned charge : -0.9999918 assigned positive charge : 342.5781 centred at (gu) : 96.69794 92.02754 98.65293 assigned negative charge : -343.5786 centred at (gu) : 96.52965 91.66420 98.88210 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 180145 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21681 grid for indexing accessible points = 1.400000 m= 89751 mr = 129374 m= 32838 mr = 72935 m= 8065 mr = 26180 m= 1249 mr = 5987 m= 71 mr = 807 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 59 time to turn everything in is 1.020000 number of dielectric boundary points 76808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 17791 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) : 1.988234 object centre at (A) : -35.55100 78.20551 65.29900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3168526 -4.7227316E-02 midg,1,midg; midg,igrid,midg -0.1569362 -0.1122284 1,midg,midg; igrid,midg,midg -0.1301205 0.3036836 gauss-seidel spectral radius is 0.9992869 estimated iterations to convergence 295 setup time was (sec) 1.290000 now iterating at: 11:33:59 rms-change max change #iterations 9.993571 404.0059 at 10iterations 5.912116 143.4779 at 20iterations 3.486089 77.35797 at 30iterations 2.048249 39.73941 at 40iterations 1.195602 24.74648 at 50iterations 0.6999211 15.49571 at 60iterations 0.4085413 7.736867 at 70iterations 0.2384912 4.594969 at 80iterations 0.1386993 2.405424 at 90iterations 8.0734372E-02 1.402364 at 100iterations 4.6991881E-02 1.101633 at 110iterations 2.7320685E-02 0.4961710 at 120iterations 1.5877308E-02 0.3454838 at 130iterations 9.2086866E-03 0.1821365 at 140iterations 5.3516147E-03 0.1018982 at 150iterations 3.1067349E-03 5.6090355E-02 at 160iterations 1.8074122E-03 3.1549454E-02 at 170iterations 1.0496918E-03 1.7723083E-02 at 180iterations finished qdiffx linear iterations at : 11:34:12 total time elapsed so far: 14.78000 # loops : 180 mean,max change (kT/e) : 1.0496918E-03 1.7723083E-02 energy calculations done at 14.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.91000 DelPhi exited at 11:34:13 14.907u 0.312s 0:15.69 96.9% 0+0k 0+0io 0pf+0w