Sat Oct 8 17:39:58 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+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 Sat Oct 8 2011 at 17:39:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3527 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 0.5256785 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): -0.9950000 44.48900 ymin,ymax (A): -30.75200 26.16900 zmin,zma (A): 1.291000 69.01300 x,y,z range (A): 45.48400 56.92100 67.72200 scale (grids/A): 0.5256785 object centre (A): 21.74700 -2.291501 35.15200 number of atom coordinates read : 3527 total number of charged atoms : 3380 net assigned charge : -5.771984 assigned positive charge : 535.1541 centred at (gu) : 90.46514 91.84345 90.60552 assigned negative charge : -540.9278 centred at (gu) : 90.42677 91.79877 90.60865 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6145 nv = 96 ne = 84 npr = 72518 no. pairs analyzed = 72518 no. exposed pairs = 4275 no. arc points = 29167 no. surface atoms = 1455 nbur = 2072 mkacc time = 0.1900000 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 = 1.624000 m= 228 mr = 3300 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2941 ## 426 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8235 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2860302E-10 -2.0053557E-10 midg,1,midg; midg,igrid,midg -2.0431203E-10 8.3019607E-12 1,midg,midg; igrid,midg,midg -2.6832189E-10 -2.2879573E-11 gauss-seidel spectral radius is 0.9813918 estimated iterations to convergence 60 setup time was (sec) 0.6300000 now iterating at: 17:39:59 rms-change max change #iterations 6.5185398E-02 9.806252 at 10iterations 4.0897145E-03 0.6923313 at 20iterations 3.8877290E-04 6.6333771E-02 at 30iterations 8.6215012E-05 1.5351295E-02 at 40iterations 2.3136154E-05 4.0771961E-03 at 50iterations finished qdiffx linear iterations at : 17:40:03 total time elapsed so far: 4.200000 # loops : 50 mean,max change (kT/e) : 2.3136154E-05 4.0771961E-03 energy calculations done at 4.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.380000 DelPhi exited at 17:40:04 4.386u 0.439s 0:05.17 93.0% 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 Sat Oct 8 2011 at 17:40:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3527 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 1.577036 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): -0.9950000 44.48900 ymin,ymax (A): -30.75200 26.16900 zmin,zma (A): 1.291000 69.01300 x,y,z range (A): 45.48400 56.92100 67.72200 scale (grids/A): 1.577036 object centre (A): 21.74700 -2.291501 35.15200 number of atom coordinates read : 3527 total number of charged atoms : 3380 net assigned charge : -5.771984 assigned positive charge : 535.1541 centred at (gu) : 91.39423 95.52943 91.81555 assigned negative charge : -540.9278 centred at (gu) : 91.28011 95.39584 91.82550 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 69729 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29167 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 20765 mr = 48836 m= 1828 mr = 14018 m= 51 mr = 823 m= 0 mr = 3 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 28693 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 409 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 25593 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) : 0.5256785 object centre at (A) : 21.74700 -2.291501 35.15200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0125396E-03 1.0466811E-02 midg,1,midg; midg,igrid,midg -8.4931767E-03 -1.2394155E-02 1,midg,midg; igrid,midg,midg -4.3841009E-03 1.0614691E-03 gauss-seidel spectral radius is 0.9980898 estimated iterations to convergence 182 setup time was (sec) 0.8600000 now iterating at: 17:40:05 rms-change max change #iterations 3.391369 148.8647 at 10iterations 1.381561 58.93037 at 20iterations 0.5649835 24.31349 at 30iterations 0.2311535 8.619057 at 40iterations 9.4184764E-02 3.148692 at 50iterations 3.8561355E-02 1.525954 at 60iterations 1.5763128E-02 0.5930300 at 70iterations 6.4830086E-03 0.2175140 at 80iterations 2.6864288E-03 9.6380129E-02 at 90iterations 1.1272102E-03 3.8791180E-02 at 100iterations 4.9192825E-04 1.8686533E-02 at 110iterations 2.2610811E-04 9.2811584E-03 at 120iterations finished qdiffx linear iterations at : 17:40:14 total time elapsed so far: 9.740000 # loops : 120 mean,max change (kT/e) : 2.2610811E-04 9.2811584E-03 energy calculations done at 9.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.910000 DelPhi exited at 17:40:14 9.918u 0.493s 0:10.68 97.3% 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 8 2011 at 17:40:14 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3527 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 2.365553 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): -0.9950000 44.48900 ymin,ymax (A): -30.75200 26.16900 zmin,zma (A): 1.291000 69.01300 x,y,z range (A): 45.48400 56.92100 67.72200 scale (grids/A): 2.365553 object centre (A): 21.74700 -2.291501 35.15200 number of atom coordinates read : 3527 total number of charged atoms : 3380 net assigned charge : -5.771984 assigned positive charge : 535.1541 centred at (gu) : 92.09099 98.29391 92.72289 assigned negative charge : -540.9278 centred at (gu) : 91.92020 98.09358 92.73814 start vw surface at 0.1400000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 162332 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29167 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 74187 mr = 119467 m= 19188 mr = 58428 m= 2638 mr = 14140 m= 122 mr = 1534 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.8100001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.360000 number of dielectric boundary points 64860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 26978 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) : 1.577036 object centre at (A) : 21.74700 -2.291501 35.15200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1904943 7.4750595E-03 midg,1,midg; midg,igrid,midg -0.1151587 -0.1676063 1,midg,midg; igrid,midg,midg -7.5776167E-02 4.4139177E-02 gauss-seidel spectral radius is 0.9991133 estimated iterations to convergence 265 setup time was (sec) 1.670000 now iterating at: 17:40:17 rms-change max change #iterations 8.959573 278.4573 at 10iterations 4.987977 115.7383 at 20iterations 2.754984 57.89536 at 30iterations 1.516613 32.63051 at 40iterations 0.8345087 17.11281 at 50iterations 0.4561884 10.54486 at 60iterations 0.2500228 5.073715 at 70iterations 0.1367559 2.805286 at 80iterations 7.4649252E-02 1.574013 at 90iterations 4.0660463E-02 0.9029880 at 100iterations 2.2170793E-02 0.4241571 at 110iterations 1.2144415E-02 0.2620659 at 120iterations 6.6176937E-03 0.1560993 at 130iterations 3.6155572E-03 7.6364517E-02 at 140iterations 1.9688392E-03 4.0687561E-02 at 150iterations 1.0814432E-03 2.1746874E-02 at 160iterations 5.9360167E-04 1.2304306E-02 at 170iterations 3.2889220E-04 7.5631142E-03 at 180iterations finished qdiffx linear iterations at : 17:40:31 total time elapsed so far: 16.40000 # loops : 180 mean,max change (kT/e) : 3.2889220E-04 7.5631142E-03 energy calculations done at 16.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.58000 DelPhi exited at 17:40:32 16.582u 0.538s 0:17.47 97.9% 0+0k 0+0io 0pf+0w