Fri Dec 30 15:57:26 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+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 Fri Dec 30 2011 at 15:57:26 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: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6640304 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): -6.541000 34.90100 ymin,ymax (A): -3.423000 48.79200 zmin,zma (A): -23.52900 30.08300 x,y,z range (A): 41.44200 52.21500 53.61200 scale (grids/A): 0.6640304 object centre (A): 14.18000 22.68450 3.277000 number of atom coordinates read : 2004 total number of charged atoms : 1871 net assigned charge : 5.3346157E-06 assigned positive charge : 294.4840 centred at (gu) : 91.10562 92.65816 90.22063 assigned negative charge : -294.4843 centred at (gu) : 91.24399 92.75748 90.14482 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6125 nv = 96 ne = 84 npr = 41282 no. pairs analyzed = 41282 no. exposed pairs = 2359 no. arc points = 17032 no. surface atoms = 801 nbur = 1203 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 330 mr = 3548 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 117 time to turn everything in is 0.1700000 number of dielectric boundary points 2860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1634 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6993 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1275230E-08 1.3785226E-08 midg,1,midg; midg,igrid,midg 9.7641282E-09 -2.7896597E-08 1,midg,midg; igrid,midg,midg 1.8424370E-08 -2.8278766E-08 gauss-seidel spectral radius is 0.9881910 estimated iterations to convergence 75 setup time was (sec) 0.3700000 now iterating at: 15:57:27 rms-change max change #iterations 0.1496857 25.68882 at 10iterations 1.6091229E-02 2.432030 at 20iterations 1.7445881E-03 0.2726555 at 30iterations 1.8748626E-04 3.0406952E-02 at 40iterations 1.9723089E-05 2.7542114E-03 at 50iterations finished qdiffx linear iterations at : 15:57:30 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.9723089E-05 2.7542114E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 15:57:30 3.342u 0.159s 0:04.20 83.0% 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 Fri Dec 30 2011 at 15:57:31 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: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 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: 1.992091 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): -6.541000 34.90100 ymin,ymax (A): -3.423000 48.79200 zmin,zma (A): -23.52900 30.08300 x,y,z range (A): 41.44200 52.21500 53.61200 scale (grids/A): 1.992091 object centre (A): 14.18000 22.68450 3.277000 number of atom coordinates read : 2004 total number of charged atoms : 1871 net assigned charge : 5.3346157E-06 assigned positive charge : 294.4840 centred at (gu) : 93.31653 97.97434 90.66189 assigned negative charge : -294.4843 centred at (gu) : 93.73209 98.27239 90.43457 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 64942 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17032 grid for indexing accessible points = 1.400000 m= 25495 mr = 45527 m= 4467 mr = 20047 m= 277 mr = 3041 m= 3 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 4274 time to turn everything in is 0.3400000 number of dielectric boundary points 26457 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 14805 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) : 0.6640304 object centre at (A) : 14.18000 22.68450 3.277000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7711468E-02 1.1669703E-02 midg,1,midg; midg,igrid,midg 3.3997625E-02 -1.2923629E-02 1,midg,midg; igrid,midg,midg 8.2130097E-03 -1.4372502E-02 gauss-seidel spectral radius is 0.9986740 estimated iterations to convergence 218 setup time was (sec) 0.5400000 now iterating at: 15:57:32 rms-change max change #iterations 3.948351 189.8187 at 10iterations 1.873091 72.59932 at 20iterations 0.8893448 29.33041 at 30iterations 0.4212758 14.69421 at 40iterations 0.1992288 7.132607 at 50iterations 9.4327614E-02 2.987961 at 60iterations 4.4725277E-02 1.470362 at 70iterations 2.1092832E-02 0.7311583 at 80iterations 9.9926256E-03 0.3168774 at 90iterations 4.7409702E-03 0.1549015 at 100iterations 2.2406208E-03 7.1061134E-02 at 110iterations 1.0638081E-03 3.3599854E-02 at 120iterations finished qdiffx linear iterations at : 15:57:39 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 1.0638081E-03 3.3599854E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 15:57:40 7.717u 0.209s 0:09.24 85.6% 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 Fri Dec 30 2011 at 15:57:40 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: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 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: 2.988137 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): -6.541000 34.90100 ymin,ymax (A): -3.423000 48.79200 zmin,zma (A): -23.52900 30.08300 x,y,z range (A): 41.44200 52.21500 53.61200 scale (grids/A): 2.988137 object centre (A): 14.18000 22.68450 3.277000 number of atom coordinates read : 2004 total number of charged atoms : 1871 net assigned charge : 5.3346157E-06 assigned positive charge : 294.4840 centred at (gu) : 94.97484 101.9616 90.99278 assigned negative charge : -294.4843 centred at (gu) : 95.59813 102.4088 90.65190 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 149656 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17032 grid for indexing accessible points = 1.400000 m= 80316 mr = 109512 m= 32301 mr = 67941 m= 8158 mr = 27241 m= 1236 mr = 6585 m= 78 mr = 862 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 14649 time to turn everything in is 0.8600000 number of dielectric boundary points 59575 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 14967 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) : 1.992091 object centre at (A) : 14.18000 22.68450 3.277000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8079439 -1.7849958E-02 midg,1,midg; midg,igrid,midg 0.3194650 -0.2043877 1,midg,midg; igrid,midg,midg 3.0336596E-02 -9.5905744E-02 gauss-seidel spectral radius is 0.9992560 estimated iterations to convergence 289 setup time was (sec) 1.080000 now iterating at: 15:57:41 rms-change max change #iterations 9.052748 523.3667 at 10iterations 5.183711 119.0793 at 20iterations 2.964741 62.66828 at 30iterations 1.700745 31.34125 at 40iterations 0.9738775 18.66734 at 50iterations 0.5569291 10.46091 at 60iterations 0.3188598 6.440348 at 70iterations 0.1820070 3.539714 at 80iterations 0.1043049 1.826345 at 90iterations 5.9598703E-02 1.130705 at 100iterations 3.4151208E-02 0.6428380 at 110iterations 1.9570541E-02 0.3922119 at 120iterations 1.1186488E-02 0.2579918 at 130iterations 6.3959369E-03 0.1143875 at 140iterations 3.6690012E-03 6.6604137E-02 at 150iterations 2.1013273E-03 4.1113377E-02 at 160iterations 1.2015352E-03 2.2513390E-02 at 170iterations 6.8855309E-04 1.3231277E-02 at 180iterations finished qdiffx linear iterations at : 15:57:52 total time elapsed so far: 12.26000 # loops : 180 mean,max change (kT/e) : 6.8855309E-04 1.3231277E-02 energy calculations done at 12.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.40000 DelPhi exited at 15:57:53 12.398u 0.218s 0:12.92 97.5% 0+0k 0+0io 0pf+0w