Tue Nov 22 14:10:11 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 Tue Nov 22 2011 at 14:10:15 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 0.6369541 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): -5.176000 35.07500 ymin,ymax (A): -3.724000 48.43800 zmin,zma (A): -24.40200 31.48900 x,y,z range (A): 40.25100 52.16200 55.89100 scale (grids/A): 0.6369541 object centre (A): 14.94950 22.35700 3.543500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 289.4000 centred at (gu) : 90.53796 92.57413 90.07677 assigned negative charge : -286.4003 centred at (gu) : 90.65540 92.71416 90.01414 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5491 nv = 96 ne = 84 npr = 40167 no. pairs analyzed = 40167 no. exposed pairs = 2502 no. arc points = 17641 no. surface atoms = 850 nbur = 1120 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 294 mr = 3067 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.1600000 number of dielectric boundary points 2688 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1738 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6432 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8180200E-10 9.3922550E-09 midg,1,midg; midg,igrid,midg 8.7828056E-09 -1.2306508E-08 1,midg,midg; igrid,midg,midg 1.1987471E-08 -5.6374110E-09 gauss-seidel spectral radius is 0.9871764 estimated iterations to convergence 72 setup time was (sec) 0.3900000 now iterating at: 14:10:18 rms-change max change #iterations 0.1188013 18.02697 at 10iterations 1.1511461E-02 1.750305 at 20iterations 1.1217771E-03 0.1939316 at 30iterations 1.0935447E-04 1.5819550E-02 at 40iterations 1.0473950E-05 1.6965866E-03 at 50iterations finished qdiffx linear iterations at : 14:10:28 total time elapsed so far: 3.680000 # loops : 50 mean,max change (kT/e) : 1.0473950E-05 1.6965866E-03 energy calculations done at 3.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.810000 DelPhi exited at 14:10:31 3.814u 0.221s 0:16.20 24.8% 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 14:10:34 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 1.910862 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): -5.176000 35.07500 ymin,ymax (A): -3.724000 48.43800 zmin,zma (A): -24.40200 31.48900 x,y,z range (A): 40.25100 52.16200 55.89100 scale (grids/A): 1.910862 object centre (A): 14.94950 22.35700 3.543500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 289.4000 centred at (gu) : 91.61405 97.72237 90.23027 assigned negative charge : -286.4003 centred at (gu) : 91.96645 98.14259 90.04261 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 58920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17641 grid for indexing accessible points = 1.400000 m= 21794 mr = 40554 m= 3124 mr = 16610 m= 133 mr = 1981 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1397 time to turn everything in is 0.3200000 number of dielectric boundary points 24785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 14467 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) : 0.6369541 object centre at (A) : 14.94950 22.35700 3.543500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3238480E-02 1.4901233E-02 midg,1,midg; midg,igrid,midg 3.2514486E-02 -8.4454780E-03 1,midg,midg; igrid,midg,midg 7.7488297E-03 -5.4171886E-03 gauss-seidel spectral radius is 0.9985673 estimated iterations to convergence 209 setup time was (sec) 0.5800000 now iterating at: 14:10:39 rms-change max change #iterations 3.579376 174.5542 at 10iterations 1.644278 64.78092 at 20iterations 0.7589541 28.19362 at 30iterations 0.3491779 12.92094 at 40iterations 0.1597168 5.594967 at 50iterations 7.3208705E-02 3.007935 at 60iterations 3.3761594E-02 1.200141 at 70iterations 1.5478373E-02 0.5711393 at 80iterations 7.1630199E-03 0.2599669 at 90iterations 3.2684368E-03 0.1181450 at 100iterations 1.5052840E-03 5.3325415E-02 at 110iterations 6.9010467E-04 2.6420116E-02 at 120iterations finished qdiffx linear iterations at : 14:11:05 total time elapsed so far: 9.250000 # loops : 120 mean,max change (kT/e) : 6.9010467E-04 2.6420116E-02 energy calculations done at 9.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.380000 DelPhi exited at 14:11:08 9.384u 0.282s 0:33.80 28.5% 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 14:11:11 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 2.866293 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): -5.176000 35.07500 ymin,ymax (A): -3.724000 48.43800 zmin,zma (A): -24.40200 31.48900 x,y,z range (A): 40.25100 52.16200 55.89100 scale (grids/A): 2.866293 object centre (A): 14.94950 22.35700 3.543500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 289.4000 centred at (gu) : 92.42105 101.5834 90.34540 assigned negative charge : -286.4003 centred at (gu) : 92.94980 102.2139 90.06392 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 135984 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17641 grid for indexing accessible points = 1.400000 m= 70091 mr = 97936 m= 25641 mr = 58371 m= 5741 mr = 21106 m= 710 mr = 4417 m= 35 mr = 468 m= 0 mr = 11 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 4993 time to turn everything in is 0.8000000 number of dielectric boundary points 55893 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 14700 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) : 1.910862 object centre at (A) : 14.94950 22.35700 3.543500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.087287 5.2449360E-02 midg,1,midg; midg,igrid,midg 0.3555857 -0.1560948 1,midg,midg; igrid,midg,midg 4.7209524E-02 -3.1116419E-02 gauss-seidel spectral radius is 0.9992256 estimated iterations to convergence 284 setup time was (sec) 1.080000 now iterating at: 14:11:17 rms-change max change #iterations 8.518648 450.8414 at 10iterations 4.905862 153.5583 at 20iterations 2.795469 69.33269 at 30iterations 1.592126 36.33628 at 40iterations 0.9043174 21.80929 at 50iterations 0.5145785 11.40864 at 60iterations 0.2916593 6.981148 at 70iterations 0.1656649 3.642820 at 80iterations 9.3682073E-02 1.855595 at 90iterations 5.3048968E-02 1.068176 at 100iterations 3.0067664E-02 0.6677704 at 110iterations 1.7044863E-02 0.3658047 at 120iterations 9.6602598E-03 0.2100067 at 130iterations 5.4737981E-03 0.1184363 at 140iterations 3.1032776E-03 6.0184479E-02 at 150iterations 1.7515820E-03 3.4965038E-02 at 160iterations 9.9199545E-04 2.1610260E-02 at 170iterations 5.6338089E-04 1.0469437E-02 at 180iterations finished qdiffx linear iterations at : 14:11:57 total time elapsed so far: 14.35000 # loops : 180 mean,max change (kT/e) : 5.6338089E-04 1.0469437E-02 energy calculations done at 14.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.46000 DelPhi exited at 14:12:00 14.463u 0.273s 0:49.53 29.7% 0+0k 0+0io 0pf+0w