Thu Feb 2 23:30:09 PST 2012 #!/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 Thu Feb 2 2012 at 23:30:09 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 ! Automatically converted by prot2crg.py # of charge parameter records: 942 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3900 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5628904 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): 3.496000 66.71301 ymin,ymax (A): 0.7010001 61.84400 zmin,zma (A): -0.7909999 62.45400 x,y,z range (A): 63.21701 61.14300 63.24500 scale (grids/A): 0.5628904 object centre (A): 35.10450 31.27250 30.83150 number of atom coordinates read : 3900 total number of charged atoms : 3747 net assigned charge : -1.499975 assigned positive charge : 587.4317 centred at (gu) : 89.39041 88.24277 88.09019 assigned negative charge : -588.9346 centred at (gu) : 89.34770 88.35917 88.01575 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8261 nv = 96 ne = 84 npr = 76188 no. pairs analyzed = 76188 no. exposed pairs = 5145 no. arc points = 35278 no. surface atoms = 1734 nbur = 2166 mkacc time = 0.1600000 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= 415 mr = 4325 m= 3 mr = 25 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 0.3200000 number of dielectric boundary points 4329 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3495 ## 345 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 10568 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2286417E-09 6.3245043E-10 midg,1,midg; midg,igrid,midg 2.5829410E-09 -1.3635238E-09 1,midg,midg; igrid,midg,midg -1.0128404E-09 4.3304921E-10 gauss-seidel spectral radius is 0.9837955 estimated iterations to convergence 65 setup time was (sec) 0.5200000 now iterating at: 23:30:10 rms-change max change #iterations 9.9690855E-02 16.22836 at 10iterations 7.7811102E-03 1.134655 at 20iterations 1.8303627E-03 0.2192001 at 30iterations 1.1012057E-03 0.1219206 at 40iterations 6.9737830E-04 7.7967644E-02 at 50iterations finished qdiffx linear iterations at : 23:30:13 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 6.9737830E-04 7.7967644E-02 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 23:30:13 3.618u 0.193s 0:04.25 89.4% 0+0k 0+46312io 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 Thu Feb 2 2012 at 23:30:14 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 ! Automatically converted by prot2crg.py # of charge parameter records: 942 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3900 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.688671 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): 3.496000 66.71301 ymin,ymax (A): 0.7010001 61.84400 zmin,zma (A): -0.7909999 62.45400 x,y,z range (A): 63.21701 61.14300 63.24500 scale (grids/A): 1.688671 object centre (A): 35.10450 31.27250 30.83150 number of atom coordinates read : 3900 total number of charged atoms : 3747 net assigned charge : -1.499975 assigned positive charge : 587.4317 centred at (gu) : 88.16989 84.72694 84.26942 assigned negative charge : -588.9346 centred at (gu) : 88.04266 85.07699 84.04666 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 91292 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35278 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 31065 mr = 62890 m= 4052 mr = 21428 m= 141 mr = 2110 m= 0 mr = 23 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 160 time to turn everything in is 0.5800000 number of dielectric boundary points 40099 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 340 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 28920 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) : 0.5628904 object centre at (A) : 35.10450 31.27250 30.83150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1887866E-02 -1.0873257E-02 midg,1,midg; midg,igrid,midg 2.3366356E-02 -2.5472259E-03 1,midg,midg; igrid,midg,midg 3.2209891E-03 1.7026245E-03 gauss-seidel spectral radius is 0.9984034 estimated iterations to convergence 199 setup time was (sec) 0.7900000 now iterating at: 23:30:15 rms-change max change #iterations 4.224931 177.5316 at 10iterations 1.856722 68.03870 at 20iterations 0.8237746 24.82915 at 30iterations 0.3628505 12.56895 at 40iterations 0.1600673 6.012047 at 50iterations 7.1076274E-02 2.176109 at 60iterations 3.1936426E-02 1.016249 at 70iterations 1.4622369E-02 0.4840549 at 80iterations 7.2515234E-03 0.2214928 at 90iterations 4.2753485E-03 0.1324749 at 100iterations 3.0695971E-03 9.2313766E-02 at 110iterations 2.4729737E-03 6.0590267E-02 at 120iterations finished qdiffx linear iterations at : 23:30:22 total time elapsed so far: 8.040000 # loops : 120 mean,max change (kT/e) : 2.4729737E-03 6.0590267E-02 energy calculations done at 8.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.190000 DelPhi exited at 23:30:22 8.198u 0.202s 0:08.70 96.4% 0+0k 0+45456io 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 Thu Feb 2 2012 at 23:30:22 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 ! Automatically converted by prot2crg.py # of charge parameter records: 942 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3900 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.533006 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): 3.496000 66.71301 ymin,ymax (A): 0.7010001 61.84400 zmin,zma (A): -0.7909999 62.45400 x,y,z range (A): 63.21701 61.14300 63.24500 scale (grids/A): 2.533006 object centre (A): 35.10450 31.27250 30.83150 number of atom coordinates read : 3900 total number of charged atoms : 3747 net assigned charge : -1.499975 assigned positive charge : 587.4317 centred at (gu) : 87.25447 82.09007 81.40383 assigned negative charge : -588.9346 centred at (gu) : 87.06396 82.61539 81.07001 start vw surface at 0.1300000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 211786 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35278 grid for indexing accessible points = 1.400000 m= 103654 mr = 153720 m= 33586 mr = 82039 m= 6713 mr = 25186 m= 617 mr = 4470 m= 12 mr = 300 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 594 time to turn everything in is 1.470000 number of dielectric boundary points 90653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 29959 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) : 1.688671 object centre at (A) : 35.10450 31.27250 30.83150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7604027 -0.1774808 midg,1,midg; midg,igrid,midg 0.3122762 -7.5478129E-02 1,midg,midg; igrid,midg,midg 0.1004339 -5.4709245E-02 gauss-seidel spectral radius is 0.9992352 estimated iterations to convergence 285 setup time was (sec) 1.710000 now iterating at: 23:30:24 rms-change max change #iterations 10.98027 400.4951 at 10iterations 6.542739 183.2011 at 20iterations 3.847552 82.41109 at 30iterations 2.247503 46.81583 at 40iterations 1.308957 25.94058 at 50iterations 0.7581638 15.20118 at 60iterations 0.4377300 8.199638 at 70iterations 0.2528385 5.720572 at 80iterations 0.1452728 2.619055 at 90iterations 8.3459169E-02 1.597115 at 100iterations 4.8039660E-02 0.8931274 at 110iterations 2.7624311E-02 0.5036488 at 120iterations 1.5969634E-02 0.3171635 at 130iterations 9.3645342E-03 0.1849999 at 140iterations 5.6245271E-03 0.1097565 at 150iterations 3.5624253E-03 6.8778992E-02 at 160iterations 2.4759613E-03 4.2249680E-02 at 170iterations 1.8956208E-03 3.4420013E-02 at 180iterations finished qdiffx linear iterations at : 23:30:36 total time elapsed so far: 13.32000 # loops : 180 mean,max change (kT/e) : 1.8956208E-03 3.4420013E-02 energy calculations done at 13.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.47000 DelPhi exited at 23:30:36 13.479u 0.219s 0:14.02 97.5% 0+0k 0+45448io 0pf+0w