Tue Nov 22 14:13:09 PST 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 Tue Nov 22 2011 at 14:13:13 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.5826800 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): -25.55200 35.54500 ymin,ymax (A): -18.87600 20.64700 zmin,zma (A): -3.495000 38.46000 x,y,z range (A): 61.09700 39.52300 41.95500 scale (grids/A): 0.5826800 object centre (A): 4.996501 0.8855000 17.48250 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.4260 centred at (gu) : 89.89561 90.17999 90.60481 assigned negative charge : -288.4263 centred at (gu) : 89.91131 90.25368 90.71653 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4443 nv = 96 ne = 84 npr = 40401 no. pairs analyzed = 40401 no. exposed pairs = 2458 no. arc points = 17434 no. surface atoms = 830 nbur = 1134 mkacc time = 8.0000006E-02 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 = 1.512000 m= 170 mr = 2376 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.2100000 number of dielectric boundary points 2225 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1823 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 5517 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1328175E-09 -1.1984438E-09 midg,1,midg; midg,igrid,midg 1.7981745E-09 -4.4572807E-10 1,midg,midg; igrid,midg,midg 1.0031985E-09 4.7822435E-10 gauss-seidel spectral radius is 0.9847122 estimated iterations to convergence 66 setup time was (sec) 0.4300000 now iterating at: 14:13:17 rms-change max change #iterations 8.2066186E-02 14.74098 at 10iterations 6.3702930E-03 1.278379 at 20iterations 5.0671247E-04 0.1079082 at 30iterations 3.9947201E-05 7.1563721E-03 at 40iterations 3.0308938E-06 6.5612793E-04 at 50iterations finished qdiffx linear iterations at : 14:13:26 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 3.0308938E-06 6.5612793E-04 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 14:13:32 3.073u 0.170s 0:18.85 17.1% 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 Tue Nov 22 2011 at 14:13:36 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.748040 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): -25.55200 35.54500 ymin,ymax (A): -18.87600 20.64700 zmin,zma (A): -3.495000 38.46000 x,y,z range (A): 61.09700 39.52300 41.95500 scale (grids/A): 1.748040 object centre (A): 4.996501 0.8855000 17.48250 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.4260 centred at (gu) : 89.68671 90.54002 91.81457 assigned negative charge : -288.4263 centred at (gu) : 89.73399 90.76121 92.14969 start vw surface at 0.1200000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 48415 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17434 grid for indexing accessible points = 1.400000 m= 16368 mr = 32877 m= 1837 mr = 12132 m= 52 mr = 1028 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1599 time to turn everything in is 0.3500000 number of dielectric boundary points 20624 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 14235 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) : 0.5826800 object centre at (A) : 4.996501 0.8855000 17.48250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8969441E-03 -4.9985489E-03 midg,1,midg; midg,igrid,midg 2.7308066E-03 -9.1180275E-04 1,midg,midg; igrid,midg,midg 3.2370821E-02 2.1380452E-02 gauss-seidel spectral radius is 0.9983033 estimated iterations to convergence 193 setup time was (sec) 0.6200000 now iterating at: 14:13:41 rms-change max change #iterations 3.026660 150.6733 at 10iterations 1.295777 60.69294 at 20iterations 0.5565969 24.44873 at 30iterations 0.2385891 10.17020 at 40iterations 0.1020216 3.917752 at 50iterations 4.3834936E-02 1.788055 at 60iterations 1.8770641E-02 0.8756714 at 70iterations 8.0799041E-03 0.3184910 at 80iterations 3.4703810E-03 0.1330070 at 90iterations 1.4912053E-03 6.1431885E-02 at 100iterations 6.3776592E-04 2.6727676E-02 at 110iterations 2.7384955E-04 1.2187958E-02 at 120iterations finished qdiffx linear iterations at : 14:13:59 total time elapsed so far: 6.640000 # loops : 120 mean,max change (kT/e) : 2.7384955E-04 1.2187958E-02 energy calculations done at 6.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.820000 DelPhi exited at 14:14:02 6.825u 0.139s 0:26.95 25.7% 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 Nov 22 2011 at 14:14:05 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.622060 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): -25.55200 35.54500 ymin,ymax (A): -18.87600 20.64700 zmin,zma (A): -3.495000 38.46000 x,y,z range (A): 61.09700 39.52300 41.95500 scale (grids/A): 2.622060 object centre (A): 4.996501 0.8855000 17.48250 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.4260 centred at (gu) : 89.52997 90.81005 92.72182 assigned negative charge : -288.4263 centred at (gu) : 89.60115 91.14177 93.22463 start vw surface at 0.1100000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 112054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17434 grid for indexing accessible points = 1.400000 m= 55087 mr = 79885 m= 17718 mr = 45239 m= 2895 mr = 14162 m= 206 mr = 2045 m= 8 mr = 114 m= 0 mr = 3 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 6009 time to turn everything in is 0.8000000 number of dielectric boundary points 46520 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 14649 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) : 1.748040 object centre at (A) : 4.996501 0.8855000 17.48250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5229779E-02 -5.3080250E-02 midg,1,midg; midg,igrid,midg 2.5732873E-02 -8.2282797E-03 1,midg,midg; igrid,midg,midg 0.3873005 0.2374462 gauss-seidel spectral radius is 0.9991451 estimated iterations to convergence 270 setup time was (sec) 1.070000 now iterating at: 14:14:14 rms-change max change #iterations 7.454068 252.2289 at 10iterations 4.140962 115.9948 at 20iterations 2.292587 56.39197 at 30iterations 1.264093 31.38562 at 40iterations 0.6978402 15.44149 at 50iterations 0.3836538 9.374997 at 60iterations 0.2104336 4.699808 at 70iterations 0.1158522 3.018961 at 80iterations 6.3483410E-02 1.467697 at 90iterations 3.4987334E-02 0.8603554 at 100iterations 1.9238111E-02 0.4207430 at 110iterations 1.0561693E-02 0.2415371 at 120iterations 5.8034132E-03 0.1435585 at 130iterations 3.1927284E-03 7.4785709E-02 at 140iterations 1.7522082E-03 3.8080215E-02 at 150iterations 9.6022896E-04 2.0694733E-02 at 160iterations 5.3028669E-04 1.3427734E-02 at 170iterations 2.9100099E-04 6.9503784E-03 at 180iterations finished qdiffx linear iterations at : 14:14:43 total time elapsed so far: 10.75000 # loops : 180 mean,max change (kT/e) : 2.9100099E-04 6.9503784E-03 energy calculations done at 10.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.91000 DelPhi exited at 14:14:46 10.917u 0.181s 0:41.43 26.7% 0+0k 0+0io 0pf+0w