Tue Oct 11 06:39:17 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 Tue Oct 11 2011 at 06:39:17 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 = 2048 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7096156 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): -20.11200 24.68900 ymin,ymax (A): -28.56900 11.07300 zmin,zma (A): -13.50600 36.66200 x,y,z range (A): 44.80100 39.64200 50.16800 scale (grids/A): 0.7096156 object centre (A): 2.288501 -8.748000 11.57800 number of atom coordinates read : 2048 total number of charged atoms : 1920 net assigned charge : 7.500009 assigned positive charge : 310.1990 centred at (gu) : 89.81344 90.57130 89.43697 assigned negative charge : -302.6992 centred at (gu) : 89.63430 90.54927 89.40389 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6966 nv = 96 ne = 84 npr = 41450 no. pairs analyzed = 41450 no. exposed pairs = 2446 no. arc points = 16680 no. surface atoms = 831 nbur = 1217 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 455 mr = 4030 m= 3 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1616 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 7724 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5676459E-08 7.5061635E-08 midg,1,midg; midg,igrid,midg 5.0210311E-08 8.6889891E-08 1,midg,midg; igrid,midg,midg -2.6004612E-08 1.4996458E-07 gauss-seidel spectral radius is 0.9896432 estimated iterations to convergence 80 setup time was (sec) 0.4600000 now iterating at: 06:39:18 rms-change max change #iterations 0.1953524 27.17276 at 10iterations 2.4697451E-02 3.535234 at 20iterations 3.2012945E-03 0.4457893 at 30iterations 4.8567090E-04 6.2875271E-02 at 40iterations 1.0464228E-04 1.5041351E-02 at 50iterations finished qdiffx linear iterations at : 06:39:20 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 1.0464228E-04 1.5041351E-02 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 06:39:21 3.246u 0.191s 0:03.97 86.3% 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 Tue Oct 11 2011 at 06:39:21 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 = 2048 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.128847 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): -20.11200 24.68900 ymin,ymax (A): -28.56900 11.07300 zmin,zma (A): -13.50600 36.66200 x,y,z range (A): 44.80100 39.64200 50.16800 scale (grids/A): 2.128847 object centre (A): 2.288501 -8.748000 11.57800 number of atom coordinates read : 2048 total number of charged atoms : 1920 net assigned charge : 7.500009 assigned positive charge : 310.1990 centred at (gu) : 89.44012 91.71403 88.31084 assigned negative charge : -302.6992 centred at (gu) : 88.90307 91.64797 88.21193 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 74107 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16680 grid for indexing accessible points = 1.400000 m= 29516 mr = 52968 m= 5689 mr = 22377 m= 524 mr = 3808 m= 9 mr = 260 m= 0 mr = 0 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 30432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 15258 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) : 0.7096156 object centre at (A) : 2.288501 -8.748000 11.57800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6354439E-02 4.6837088E-02 midg,1,midg; midg,igrid,midg 4.8968927E-03 3.3945523E-02 1,midg,midg; igrid,midg,midg 1.7285841E-02 4.0669508E-02 gauss-seidel spectral radius is 0.9988323 estimated iterations to convergence 232 setup time was (sec) 0.8600000 now iterating at: 06:39:22 rms-change max change #iterations 4.544088 208.6606 at 10iterations 2.244465 83.12837 at 20iterations 1.116803 37.29824 at 30iterations 0.5547982 16.95930 at 40iterations 0.2756574 8.484741 at 50iterations 0.1370694 4.645699 at 60iterations 6.8114370E-02 2.049713 at 70iterations 3.4016680E-02 1.018030 at 80iterations 1.6979281E-02 0.5250244 at 90iterations 8.5138651E-03 0.2345581 at 100iterations 4.2644702E-03 0.1284494 at 110iterations 2.1830508E-03 6.2422752E-02 at 120iterations finished qdiffx linear iterations at : 06:39:28 total time elapsed so far: 7.290000 # loops : 120 mean,max change (kT/e) : 2.1830508E-03 6.2422752E-02 energy calculations done at 7.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 06:39:29 7.459u 0.210s 0:08.21 93.3% 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 Tue Oct 11 2011 at 06:39:29 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 = 2048 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.193270 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): -20.11200 24.68900 ymin,ymax (A): -28.56900 11.07300 zmin,zma (A): -13.50600 36.66200 x,y,z range (A): 44.80100 39.64200 50.16800 scale (grids/A): 3.193270 object centre (A): 2.288501 -8.748000 11.57800 number of atom coordinates read : 2048 total number of charged atoms : 1920 net assigned charge : 7.500009 assigned positive charge : 310.1990 centred at (gu) : 89.16025 92.57107 87.46635 assigned negative charge : -302.6992 centred at (gu) : 88.35468 92.47203 87.31794 start vw surface at 0.1200000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 170881 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16680 grid for indexing accessible points = 1.400000 m= 92257 mr = 127437 m= 37236 mr = 76756 m= 10776 mr = 30725 m= 2124 mr = 8336 m= 230 mr = 1516 m= 7 mr = 138 m= 0 mr = 4 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.690000 number of dielectric boundary points 68599 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 15360 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) : 2.128847 object centre at (A) : 2.288501 -8.748000 11.57800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7205305 0.3829320 midg,1,midg; midg,igrid,midg 2.1129867E-02 0.2631746 1,midg,midg; igrid,midg,midg 0.2937711 0.3035525 gauss-seidel spectral radius is 0.9992906 estimated iterations to convergence 296 setup time was (sec) 2.000000 now iterating at: 06:39:31 rms-change max change #iterations 10.11764 402.6567 at 10iterations 5.978154 137.1168 at 20iterations 3.526696 65.94264 at 30iterations 2.076527 39.97913 at 40iterations 1.219203 22.21261 at 50iterations 0.7161489 13.99141 at 60iterations 0.4189968 7.739333 at 70iterations 0.2454528 4.598379 at 80iterations 0.1439641 2.989908 at 90iterations 8.4108241E-02 1.640858 at 100iterations 4.9248543E-02 0.9236460 at 110iterations 2.8892083E-02 0.5005751 at 120iterations 1.6953370E-02 0.2962440 at 130iterations 1.0072262E-02 0.1899834 at 140iterations 6.0751084E-03 0.1106510 at 150iterations 3.7444106E-03 6.7252159E-02 at 160iterations 2.4137627E-03 5.0842285E-02 at 170iterations 1.6412552E-03 2.9701233E-02 at 180iterations finished qdiffx linear iterations at : 06:39:42 total time elapsed so far: 12.19000 # loops : 180 mean,max change (kT/e) : 1.6412552E-03 2.9701233E-02 energy calculations done at 12.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.36000 DelPhi exited at 06:39:42 12.360u 0.224s 0:13.06 96.3% 0+0k 0+0io 0pf+0w