Wed Feb 15 08:56:01 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_thinner.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 Wed Feb 15 2012 at 08:56:01 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: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2466 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.6746001 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): -22.27700 27.31300 ymin,ymax (A): 3.700000 44.70200 zmin,zma (A): -2.500000 50.27200 x,y,z range (A): 49.59000 41.00200 52.77200 scale (grids/A): 0.6746001 object centre (A): 2.518000 24.20100 23.88600 number of atom coordinates read : 2466 total number of charged atoms : 2332 net assigned charge : 8.7916851E-06 assigned positive charge : 359.8650 centred at (gu) : 90.68784 90.84158 90.77227 assigned negative charge : -359.8660 centred at (gu) : 90.62422 90.79726 90.78636 start vw surface at 0.2500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 7684 nv = 96 ne = 84 npr = 51060 no. pairs analyzed = 51060 no. exposed pairs = 3375 no. arc points = 23104 no. surface atoms = 1132 nbur = 1334 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 470 mr = 4064 m= 3 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 4031 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2100 ## 190 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8811 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9948255E-09 -4.6214801E-09 midg,1,midg; midg,igrid,midg -1.0052832E-08 1.3663077E-08 1,midg,midg; igrid,midg,midg -1.4844739E-08 1.9046212E-08 gauss-seidel spectral radius is 0.9886019 estimated iterations to convergence 76 setup time was (sec) 0.6800000 now iterating at: 08:56:02 rms-change max change #iterations 0.1740285 26.50029 at 10iterations 1.9479347E-02 2.574776 at 20iterations 2.1886653E-03 0.2776718 at 30iterations 2.5594770E-04 3.1909943E-02 at 40iterations 3.5320947E-05 4.4040680E-03 at 50iterations finished qdiffx linear iterations at : 08:56:05 total time elapsed so far: 3.730000 # loops : 50 mean,max change (kT/e) : 3.5320947E-05 4.4040680E-03 energy calculations done at 3.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.990000 DelPhi exited at 08:56:07 3.992u 0.273s 0:07.99 53.3% 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 Wed Feb 15 2012 at 08:56:09 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: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2466 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: 2.023800 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): -22.27700 27.31300 ymin,ymax (A): 3.700000 44.70200 zmin,zma (A): -2.500000 50.27200 x,y,z range (A): 49.59000 41.00200 52.77200 scale (grids/A): 2.023800 object centre (A): 2.518000 24.20100 23.88600 number of atom coordinates read : 2466 total number of charged atoms : 2332 net assigned charge : 8.7916851E-06 assigned positive charge : 359.8650 centred at (gu) : 92.06297 92.52424 92.31648 assigned negative charge : -359.8660 centred at (gu) : 91.87270 92.39168 92.35933 start vw surface at 0.2200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 81690 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23104 grid for indexing accessible points = 1.400000 m= 30103 mr = 55586 m= 5416 mr = 21344 m= 435 mr = 3302 m= 6 mr = 191 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 137 time to turn everything in is 0.7200000 number of dielectric boundary points 37227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 18463 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) : 0.6746001 object centre at (A) : 2.518000 24.20100 23.88600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2022715E-02 1.1777669E-02 midg,1,midg; midg,igrid,midg -1.7653596E-02 2.9941485E-03 1,midg,midg; igrid,midg,midg 1.1234715E-02 1.4709294E-02 gauss-seidel spectral radius is 0.9987798 estimated iterations to convergence 227 setup time was (sec) 1.030000 now iterating at: 08:56:11 rms-change max change #iterations 4.606164 218.9341 at 10iterations 2.241969 69.10892 at 20iterations 1.091676 34.76049 at 30iterations 0.5330821 15.25281 at 40iterations 0.2604583 7.884487 at 50iterations 0.1274811 3.757178 at 60iterations 6.2129173E-02 1.926521 at 70iterations 3.0435037E-02 0.9210358 at 80iterations 1.4848989E-02 0.4586506 at 90iterations 7.2158109E-03 0.2234364 at 100iterations 3.5471590E-03 9.6332550E-02 at 110iterations 1.7322062E-03 5.7265043E-02 at 120iterations finished qdiffx linear iterations at : 08:56:18 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 1.7322062E-03 5.7265043E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.270000 DelPhi exited at 08:56:18 8.271u 0.323s 0:09.10 94.3% 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 Wed Feb 15 2012 at 08:56:18 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: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2466 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: 3.035701 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): -22.27700 27.31300 ymin,ymax (A): 3.700000 44.70200 zmin,zma (A): -2.500000 50.27200 x,y,z range (A): 49.59000 41.00200 52.77200 scale (grids/A): 3.035701 object centre (A): 2.518000 24.20100 23.88600 number of atom coordinates read : 2466 total number of charged atoms : 2332 net assigned charge : 8.7916851E-06 assigned positive charge : 359.8650 centred at (gu) : 93.09435 93.78630 93.47448 assigned negative charge : -359.8660 centred at (gu) : 92.80905 93.58753 93.53904 start vw surface at 0.1600000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 188808 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23104 grid for indexing accessible points = 1.400000 m= 94849 mr = 135179 m= 36704 mr = 75810 m= 9921 mr = 28792 m= 1788 mr = 7279 m= 151 mr = 1200 m= 3 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 445 time to turn everything in is 1.640000 number of dielectric boundary points 83885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 18656 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) : 2.023800 object centre at (A) : 2.518000 24.20100 23.88600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7539347E-02 4.8127659E-02 midg,1,midg; midg,igrid,midg -0.1910789 -4.6795625E-02 1,midg,midg; igrid,midg,midg 0.3052070 0.2138012 gauss-seidel spectral radius is 0.9993089 estimated iterations to convergence 300 setup time was (sec) 1.960000 now iterating at: 08:56:21 rms-change max change #iterations 10.69999 529.1072 at 10iterations 6.405161 173.3790 at 20iterations 3.833589 73.94752 at 30iterations 2.273922 42.52157 at 40iterations 1.350104 25.56497 at 50iterations 0.7988217 14.53158 at 60iterations 0.4721529 9.586418 at 70iterations 0.2784860 4.887007 at 80iterations 0.1638770 2.733824 at 90iterations 9.6424602E-02 1.742534 at 100iterations 5.6639817E-02 0.9907169 at 110iterations 3.3311028E-02 0.6454649 at 120iterations 1.9566331E-02 0.3432994 at 130iterations 1.1491259E-02 0.2217140 at 140iterations 6.7595229E-03 0.1318741 at 150iterations 3.9721616E-03 6.8052292E-02 at 160iterations 2.3477604E-03 3.8810730E-02 at 170iterations 1.3895411E-03 2.4988174E-02 at 180iterations finished qdiffx linear iterations at : 08:56:32 total time elapsed so far: 13.24000 # loops : 180 mean,max change (kT/e) : 1.3895411E-03 2.4988174E-02 energy calculations done at 13.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.44000 DelPhi exited at 08:56:33 13.440u 0.252s 0:14.28 95.8% 0+0k 0+0io 0pf+0w