Sun Oct 9 06:18:46 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 Sun Oct 9 2011 at 06:18:47 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1990 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NAP 187 has a net charge of -2.0000 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: 0.6691855 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): 1.995000 44.34700 ymin,ymax (A): -9.072001 37.87800 zmin,zma (A): -24.49100 28.70800 x,y,z range (A): 42.35200 46.95000 53.19900 scale (grids/A): 0.6691855 object centre (A): 23.17100 14.40300 2.108500 number of atom coordinates read : 1990 total number of charged atoms : 1851 net assigned charge : -1.499986 assigned positive charge : 299.4321 centred at (gu) : 90.12434 89.30289 88.48692 assigned negative charge : -300.9321 centred at (gu) : 89.96727 89.13908 88.44302 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6078 nv = 96 ne = 84 npr = 41521 no. pairs analyzed = 41521 no. exposed pairs = 2546 no. arc points = 17895 no. surface atoms = 858 nbur = 1132 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 371 mr = 3304 m= 0 mr = 66 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.2500000 number of dielectric boundary points 3079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1731 ## 153 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6996 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7737648E-08 2.8414311E-09 midg,1,midg; midg,igrid,midg -4.2353633E-08 2.2973367E-08 1,midg,midg; igrid,midg,midg -3.4357150E-08 2.6031071E-08 gauss-seidel spectral radius is 0.9883712 estimated iterations to convergence 76 setup time was (sec) 0.4900000 now iterating at: 06:18:47 rms-change max change #iterations 0.1537272 25.66226 at 10iterations 1.7016198E-02 2.850452 at 20iterations 1.8340281E-03 0.2439337 at 30iterations 2.0353618E-04 2.9117584E-02 at 40iterations 2.2118405E-05 4.2114258E-03 at 50iterations finished qdiffx linear iterations at : 06:18:50 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 2.2118405E-05 4.2114258E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 06:18:50 3.344u 0.207s 0:03.85 91.9% 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 Sun Oct 9 2011 at 06:18:50 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1990 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NAP 187 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.007556 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): 1.995000 44.34700 ymin,ymax (A): -9.072001 37.87800 zmin,zma (A): -24.49100 28.70800 x,y,z range (A): 42.35200 46.95000 53.19900 scale (grids/A): 2.007556 object centre (A): 23.17100 14.40300 2.108500 number of atom coordinates read : 1990 total number of charged atoms : 1851 net assigned charge : -1.499986 assigned positive charge : 299.4321 centred at (gu) : 90.37300 87.90864 85.46056 assigned negative charge : -300.9321 centred at (gu) : 89.90198 87.41750 85.32911 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 64643 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17895 grid for indexing accessible points = 1.400000 m= 24418 mr = 44095 m= 4473 mr = 18363 m= 368 mr = 3055 m= 11 mr = 164 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1987 time to turn everything in is 0.4800000 number of dielectric boundary points 28236 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 14619 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) : 0.6691855 object centre at (A) : 23.17100 14.40300 2.108500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0597472E-02 2.7232256E-02 midg,1,midg; midg,igrid,midg -3.2894172E-02 1.3767879E-02 1,midg,midg; igrid,midg,midg -3.0973796E-02 1.5900314E-02 gauss-seidel spectral radius is 0.9987078 estimated iterations to convergence 220 setup time was (sec) 0.7400000 now iterating at: 06:18:51 rms-change max change #iterations 4.137961 256.0540 at 10iterations 1.962103 86.60985 at 20iterations 0.9400989 31.05786 at 30iterations 0.4488354 16.00182 at 40iterations 0.2138408 7.128335 at 50iterations 0.1020220 3.254625 at 60iterations 4.8811719E-02 1.702290 at 70iterations 2.3298135E-02 0.7367249 at 80iterations 1.1138975E-02 0.3728323 at 90iterations 5.3316345E-03 0.1867914 at 100iterations 2.5484662E-03 8.5289001E-02 at 110iterations 1.2123747E-03 4.2819262E-02 at 120iterations finished qdiffx linear iterations at : 06:18:57 total time elapsed so far: 6.610000 # loops : 120 mean,max change (kT/e) : 1.2123747E-03 4.2819262E-02 energy calculations done at 6.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.800000 DelPhi exited at 06:18:58 6.805u 0.189s 0:07.29 95.7% 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 Sun Oct 9 2011 at 06:18:58 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1990 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NAP 187 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.011335 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): 1.995000 44.34700 ymin,ymax (A): -9.072001 37.87800 zmin,zma (A): -24.49100 28.70800 x,y,z range (A): 42.35200 46.95000 53.19900 scale (grids/A): 3.011335 object centre (A): 23.17100 14.40300 2.108500 number of atom coordinates read : 1990 total number of charged atoms : 1851 net assigned charge : -1.499986 assigned positive charge : 299.4321 centred at (gu) : 90.55941 86.86306 83.19095 assigned negative charge : -300.9321 centred at (gu) : 89.85292 86.12634 82.99367 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 148769 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17895 grid for indexing accessible points = 1.400000 m= 77333 mr = 106106 m= 30092 mr = 63959 m= 8406 mr = 24732 m= 1563 mr = 6667 m= 153 mr = 1128 m= 6 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 6867 time to turn everything in is 1.210000 number of dielectric boundary points 63653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 14808 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) : 2.007556 object centre at (A) : 23.17100 14.40300 2.108500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4990108 0.8715906 midg,1,midg; midg,igrid,midg -0.3039958 0.1641795 1,midg,midg; igrid,midg,midg -0.2993229 0.1121115 gauss-seidel spectral radius is 0.9992625 estimated iterations to convergence 291 setup time was (sec) 1.520000 now iterating at: 06:18:59 rms-change max change #iterations 9.416680 410.4917 at 10iterations 5.434508 132.5536 at 20iterations 3.130741 72.25616 at 30iterations 1.805536 38.55857 at 40iterations 1.041450 20.70901 at 50iterations 0.5982668 12.39154 at 60iterations 0.3445622 7.048588 at 70iterations 0.1973958 4.184492 at 80iterations 0.1136008 2.120712 at 90iterations 6.5065637E-02 1.247343 at 100iterations 3.7327070E-02 0.7226186 at 110iterations 2.1465687E-02 0.4392595 at 120iterations 1.2318459E-02 0.2340641 at 130iterations 7.0806127E-03 0.1403122 at 140iterations 4.0571438E-03 9.1690063E-02 at 150iterations 2.3377179E-03 4.5840263E-02 at 160iterations 1.3434098E-03 2.6100159E-02 at 170iterations 7.6875981E-04 1.4802933E-02 at 180iterations finished qdiffx linear iterations at : 06:19:10 total time elapsed so far: 12.07000 # loops : 180 mean,max change (kT/e) : 7.6875981E-04 1.4802933E-02 energy calculations done at 12.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.25000 DelPhi exited at 06:19:11 12.249u 0.244s 0:12.76 97.8% 0+0k 0+0io 0pf+0w