Sat Oct 15 10:24:06 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+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 Sat Oct 15 2011 at 10:24:06 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4468 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5909008 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): -24.86600 34.95700 ymin,ymax (A): 34.79300 95.04000 zmin,zma (A): 30.38600 89.43100 x,y,z range (A): 59.82300 60.24700 59.04500 scale (grids/A): 0.5909008 object centre (A): 5.045499 64.91650 59.90850 number of atom coordinates read : 4468 total number of charged atoms : 4309 net assigned charge : -1.999937 assigned positive charge : 673.7538 centred at (gu) : 90.48557 89.23101 88.84197 assigned negative charge : -675.7571 centred at (gu) : 90.35187 89.38843 88.99896 start vw surface at 0.2200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 9934 nv = 96 ne = 84 npr = 94754 no. pairs analyzed = 94754 no. exposed pairs = 5000 no. arc points = 34004 no. surface atoms = 1703 nbur = 2765 mkacc time = 0.2700000 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 = 1.456000 m= 492 mr = 5820 m= 4 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 170 time to turn everything in is 0.5500000 number of dielectric boundary points 4540 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3672 ## 414 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 13099 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.5995202E-09 -6.4471455E-09 midg,1,midg; midg,igrid,midg 7.8616713E-09 -7.0714026E-09 1,midg,midg; igrid,midg,midg -6.5081642E-09 6.1261529E-09 gauss-seidel spectral radius is 0.9853207 estimated iterations to convergence 68 setup time was (sec) 0.8300000 now iterating at: 10:24:07 rms-change max change #iterations 0.1333435 18.55617 at 10iterations 1.1519789E-02 1.380119 at 20iterations 1.2641458E-03 0.1577530 at 30iterations 2.9506607E-04 3.2020569E-02 at 40iterations 1.0228365E-04 1.2418747E-02 at 50iterations finished qdiffx linear iterations at : 10:24:11 total time elapsed so far: 4.230000 # loops : 50 mean,max change (kT/e) : 1.0228365E-04 1.2418747E-02 energy calculations done at 4.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.410000 DelPhi exited at 10:24:11 4.413u 0.285s 0:05.16 90.8% 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 Sat Oct 15 2011 at 10:24:12 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4468 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.772702 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): -24.86600 34.95700 ymin,ymax (A): 34.79300 95.04000 zmin,zma (A): 30.38600 89.43100 x,y,z range (A): 59.82300 60.24700 59.04500 scale (grids/A): 1.772702 object centre (A): 5.045499 64.91650 59.90850 number of atom coordinates read : 4468 total number of charged atoms : 4309 net assigned charge : -1.999937 assigned positive charge : 673.7538 centred at (gu) : 91.45554 87.69171 86.52457 assigned negative charge : -675.7571 centred at (gu) : 91.05520 88.16470 86.99657 start vw surface at 0.2100000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 110644 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34004 grid for indexing accessible points = 1.400000 m= 38554 mr = 80592 m= 5354 mr = 28705 m= 249 mr = 3431 m= 4 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 8586 time to turn everything in is 0.9500000 number of dielectric boundary points 42001 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 346 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 33531 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) : 0.5909008 object centre at (A) : 5.045499 64.91650 59.90850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7627520E-02 -3.9157115E-02 midg,1,midg; midg,igrid,midg 3.6275260E-02 -2.1742266E-02 1,midg,midg; igrid,midg,midg -7.9323407E-03 3.9059639E-02 gauss-seidel spectral radius is 0.9985901 estimated iterations to convergence 211 setup time was (sec) 1.270000 now iterating at: 10:24:13 rms-change max change #iterations 5.080577 198.3503 at 10iterations 2.343526 67.79879 at 20iterations 1.083832 28.72759 at 30iterations 0.5022010 15.35556 at 40iterations 0.2324363 6.248077 at 50iterations 0.1079358 2.820856 at 60iterations 5.0081439E-02 1.359386 at 70iterations 2.3302438E-02 0.6355362 at 80iterations 1.0837213E-02 0.3012657 at 90iterations 5.0520212E-03 0.1297417 at 100iterations 2.3888680E-03 6.3523293E-02 at 110iterations 1.1467267E-03 2.9033661E-02 at 120iterations finished qdiffx linear iterations at : 10:24:22 total time elapsed so far: 10.15000 # loops : 120 mean,max change (kT/e) : 1.1467267E-03 2.9033661E-02 energy calculations done at 10.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.34000 DelPhi exited at 10:24:23 10.347u 0.326s 0:11.27 94.5% 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 Sat Oct 15 2011 at 10:24:23 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4468 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.659054 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): -24.86600 34.95700 ymin,ymax (A): 34.79300 95.04000 zmin,zma (A): 30.38600 89.43100 x,y,z range (A): 59.82300 60.24700 59.04500 scale (grids/A): 2.659054 object centre (A): 5.045499 64.91650 59.90850 number of atom coordinates read : 4468 total number of charged atoms : 4309 net assigned charge : -1.999937 assigned positive charge : 673.7538 centred at (gu) : 92.18290 86.53728 84.78644 assigned negative charge : -675.7571 centred at (gu) : 91.58263 87.24683 85.49464 start vw surface at 0.2000000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 257103 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34004 grid for indexing accessible points = 1.400000 m= 129244 mr = 195569 m= 42803 mr = 107138 m= 9271 mr = 34448 m= 1085 mr = 7016 m= 53 mr = 732 m= 0 mr = 26 time to grow re-entrant surface = 1.490000 no. cavity mid-points inaccessible to solvent = 29106 time to turn everything in is 2.440000 number of dielectric boundary points 94630 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 2.610000 number of grid points assigned charge 34457 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) : 1.772702 object centre at (A) : 5.045499 64.91650 59.90850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4212283 -0.4478518 midg,1,midg; midg,igrid,midg 0.4053279 -0.4407652 1,midg,midg; igrid,midg,midg 3.9209165E-03 0.3189880 gauss-seidel spectral radius is 0.9992750 estimated iterations to convergence 293 setup time was (sec) 2.790000 now iterating at: 10:24:26 rms-change max change #iterations 12.20577 269.3509 at 10iterations 7.238920 146.9649 at 20iterations 4.242671 87.67681 at 30iterations 2.482560 45.54129 at 40iterations 1.453973 24.14592 at 50iterations 0.8458220 14.01219 at 60iterations 0.4924866 8.192757 at 70iterations 0.2859220 4.759357 at 80iterations 0.1659667 2.597635 at 90iterations 9.6376762E-02 1.515474 at 100iterations 5.5948958E-02 0.8851705 at 110iterations 3.2452695E-02 0.5189381 at 120iterations 1.8856287E-02 0.2851978 at 130iterations 1.0967448E-02 0.1891513 at 140iterations 6.4170873E-03 9.8670959E-02 at 150iterations 3.7731640E-03 6.9558412E-02 at 160iterations 2.2634708E-03 3.6346436E-02 at 170iterations 1.3862717E-03 2.2277832E-02 at 180iterations finished qdiffx linear iterations at : 10:24:41 total time elapsed so far: 17.99000 # loops : 180 mean,max change (kT/e) : 1.3862717E-03 2.2277832E-02 energy calculations done at 17.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.17000 DelPhi exited at 10:24:42 18.176u 0.375s 0:18.98 97.6% 0+0k 0+0io 0pf+0w