Mon Oct 10 17:09:11 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 Mon Oct 10 2011 at 17:09:11 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4295 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5111932 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): -15.91300 36.49600 ymin,ymax (A): -32.13100 31.23000 zmin,zma (A): -3.978000 65.66300 x,y,z range (A): 52.40900 63.36100 69.64100 scale (grids/A): 0.5111932 object centre (A): 10.29150 -0.4505005 30.84250 number of atom coordinates read : 4295 total number of charged atoms : 4047 net assigned charge : 4.606028 assigned positive charge : 638.4683 centred at (gu) : 90.24358 90.75291 87.62627 assigned negative charge : -633.8661 centred at (gu) : 90.11765 90.80499 87.64799 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7084 nv = 96 ne = 84 npr = 87436 no. pairs analyzed = 87436 no. exposed pairs = 5514 no. arc points = 38128 no. surface atoms = 1845 nbur = 2450 mkacc time = 0.2900000 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 = 1.652000 m= 250 mr = 3596 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 3728 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3649 ## 540 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 9420 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1801951E-10 8.8027138E-12 midg,1,midg; midg,igrid,midg 1.5335247E-10 -7.0719819E-11 1,midg,midg; igrid,midg,midg -2.1942670E-10 3.7949160E-10 gauss-seidel spectral radius is 0.9803951 estimated iterations to convergence 59 setup time was (sec) 0.8600000 now iterating at: 17:09:12 rms-change max change #iterations 6.5906487E-02 10.99675 at 10iterations 3.9627193E-03 0.7865868 at 20iterations 4.2954012E-04 5.8266759E-02 at 30iterations 1.2953980E-04 1.8267468E-02 at 40iterations 4.7158508E-05 6.9162846E-03 at 50iterations finished qdiffx linear iterations at : 17:09:16 total time elapsed so far: 4.460000 # loops : 50 mean,max change (kT/e) : 4.7158508E-05 6.9162846E-03 energy calculations done at 4.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.680000 DelPhi exited at 17:09:17 4.684u 0.431s 0:06.32 80.8% 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 Mon Oct 10 2011 at 17:09:18 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 # of charge parameter records: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4295 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.533579 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): -15.91300 36.49600 ymin,ymax (A): -32.13100 31.23000 zmin,zma (A): -3.978000 65.66300 x,y,z range (A): 52.40900 63.36100 69.64100 scale (grids/A): 1.533579 object centre (A): 10.29150 -0.4505005 30.84250 number of atom coordinates read : 4295 total number of charged atoms : 4047 net assigned charge : 4.606028 assigned positive charge : 638.4683 centred at (gu) : 90.72972 92.25735 82.87723 assigned negative charge : -633.8661 centred at (gu) : 90.35278 92.41463 82.94370 start vw surface at 0.2100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 79797 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38128 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 22689 mr = 54262 m= 1952 mr = 14802 m= 30 mr = 796 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 54 time to turn everything in is 0.8300000 number of dielectric boundary points 34608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 436 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 30388 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) : 0.5111932 object centre at (A) : 10.29150 -0.4505005 30.84250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1498241E-03 8.7753963E-03 midg,1,midg; midg,igrid,midg -6.8978890E-04 -9.8987259E-03 1,midg,midg; igrid,midg,midg -3.1004767E-03 9.0836650E-03 gauss-seidel spectral radius is 0.9980695 estimated iterations to convergence 181 setup time was (sec) 1.150000 now iterating at: 17:09:19 rms-change max change #iterations 3.541582 189.0519 at 10iterations 1.429879 50.08037 at 20iterations 0.5804808 19.02632 at 30iterations 0.2354331 7.981667 at 40iterations 9.5208570E-02 3.118408 at 50iterations 3.8945526E-02 1.364655 at 60iterations 1.5787655E-02 0.5808229 at 70iterations 6.4503225E-03 0.2376709 at 80iterations 2.6438623E-03 8.2859039E-02 at 90iterations 1.1063003E-03 3.5231590E-02 at 100iterations 4.8082328E-04 1.8943787E-02 at 110iterations 2.2736446E-04 8.5515976E-03 at 120iterations finished qdiffx linear iterations at : 17:09:28 total time elapsed so far: 10.12000 # loops : 120 mean,max change (kT/e) : 2.2736446E-04 8.5515976E-03 energy calculations done at 10.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.33000 DelPhi exited at 17:09:29 10.339u 0.502s 0:11.41 94.9% 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 Mon Oct 10 2011 at 17:09:29 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4295 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.300369 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): -15.91300 36.49600 ymin,ymax (A): -32.13100 31.23000 zmin,zma (A): -3.978000 65.66300 x,y,z range (A): 52.40900 63.36100 69.64100 scale (grids/A): 2.300369 object centre (A): 10.29150 -0.4505005 30.84250 number of atom coordinates read : 4295 total number of charged atoms : 4047 net assigned charge : 4.606028 assigned positive charge : 638.4683 centred at (gu) : 91.09409 93.38574 79.31551 assigned negative charge : -633.8661 centred at (gu) : 90.52905 93.62196 79.41540 start vw surface at 0.2100000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 186376 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38128 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 81540 mr = 133772 m= 20092 mr = 63201 m= 2910 mr = 14287 m= 140 mr = 1695 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 177 time to turn everything in is 2.010000 number of dielectric boundary points 78060 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 32305 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) : 1.533579 object centre at (A) : 10.29150 -0.4505005 30.84250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1606413 0.2475993 midg,1,midg; midg,igrid,midg -7.9513550E-02 -0.2402997 1,midg,midg; igrid,midg,midg -4.0330544E-02 0.1253816 gauss-seidel spectral radius is 0.9991392 estimated iterations to convergence 269 setup time was (sec) 2.410000 now iterating at: 17:09:32 rms-change max change #iterations 9.623116 275.7156 at 10iterations 5.455735 120.4935 at 20iterations 3.074957 63.54771 at 30iterations 1.724890 39.98901 at 40iterations 0.9662151 24.14710 at 50iterations 0.5382255 10.90271 at 60iterations 0.2992696 6.547282 at 70iterations 0.1657398 3.349886 at 80iterations 9.1992408E-02 2.046564 at 90iterations 5.0853759E-02 1.024604 at 100iterations 2.8140564E-02 0.5684149 at 110iterations 1.5529239E-02 0.3195496 at 120iterations 8.5886614E-03 0.1914711 at 130iterations 4.7433958E-03 9.7297668E-02 at 140iterations 2.6207699E-03 6.1462402E-02 at 150iterations 1.4520523E-03 2.7634621E-02 at 160iterations 8.0420211E-04 1.7269135E-02 at 170iterations 4.4940284E-04 9.3164444E-03 at 180iterations finished qdiffx linear iterations at : 17:09:47 total time elapsed so far: 17.57000 # loops : 180 mean,max change (kT/e) : 4.4940284E-04 9.3164444E-03 energy calculations done at 17.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.79000 DelPhi exited at 17:09:48 17.793u 0.479s 0:18.57 98.3% 0+0k 0+0io 0pf+0w