Wed Dec 21 14:20:48 PST 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 Wed Dec 21 2011 at 14:20:48 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1953 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6478853 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): -6.227000 30.89700 ymin,ymax (A): -46.66200 7.556000 zmin,zma (A): -54.51700 0.4310000 x,y,z range (A): 37.12400 54.21800 54.94800 scale (grids/A): 0.6478853 object centre (A): 12.33500 -19.55300 -27.04300 number of atom coordinates read : 1953 total number of charged atoms : 1820 net assigned charge : 2.681006 assigned positive charge : 286.6021 centred at (gu) : 90.04911 92.15902 89.84158 assigned negative charge : -283.9213 centred at (gu) : 89.93321 92.31171 89.93244 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5718 nv = 96 ne = 84 npr = 39334 no. pairs analyzed = 39334 no. exposed pairs = 2557 no. arc points = 17714 no. surface atoms = 867 nbur = 1086 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 321 mr = 3136 m= 3 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 2870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1760 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6583 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5190517E-08 -4.2210986E-09 midg,1,midg; midg,igrid,midg 1.3342515E-08 -1.7916973E-08 1,midg,midg; igrid,midg,midg -6.9850326E-09 1.7437809E-08 gauss-seidel spectral radius is 0.9876012 estimated iterations to convergence 73 setup time was (sec) 0.3600000 now iterating at: 14:20:49 rms-change max change #iterations 0.1272633 19.74733 at 10iterations 1.2931348E-02 2.007116 at 20iterations 1.3270781E-03 0.2068138 at 30iterations 1.3556308E-04 2.5236130E-02 at 40iterations 1.3496867E-05 2.1867752E-03 at 50iterations finished qdiffx linear iterations at : 14:20:52 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 1.3496867E-05 2.1867752E-03 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 14:20:52 3.586u 0.272s 0:04.16 92.5% 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 Dec 21 2011 at 14:20:52 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1953 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.943656 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): -6.227000 30.89700 ymin,ymax (A): -46.66200 7.556000 zmin,zma (A): -54.51700 0.4310000 x,y,z range (A): 37.12400 54.21800 54.94800 scale (grids/A): 1.943656 object centre (A): 12.33500 -19.55300 -27.04300 number of atom coordinates read : 1953 total number of charged atoms : 1820 net assigned charge : 2.681006 assigned positive charge : 286.6021 centred at (gu) : 90.14758 96.47730 89.52450 assigned negative charge : -283.9213 centred at (gu) : 89.79974 96.93542 89.79754 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 61029 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17714 grid for indexing accessible points = 1.400000 m= 22796 mr = 41756 m= 3674 mr = 17158 m= 231 mr = 2362 m= 6 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 261 time to turn everything in is 0.3200000 number of dielectric boundary points 26368 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 14357 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) : 0.6478853 object centre at (A) : 12.33500 -19.55300 -27.04300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1502338E-02 4.6143755E-02 midg,1,midg; midg,igrid,midg 4.0844914E-02 -1.9758129E-02 1,midg,midg; igrid,midg,midg -4.4363192E-03 6.8543633E-03 gauss-seidel spectral radius is 0.9986156 estimated iterations to convergence 213 setup time was (sec) 0.5700000 now iterating at: 14:20:53 rms-change max change #iterations 3.695133 198.6145 at 10iterations 1.721666 67.88445 at 20iterations 0.8045468 29.98486 at 30iterations 0.3733739 13.17820 at 40iterations 0.1738949 5.974030 at 50iterations 8.0522373E-02 2.813293 at 60iterations 3.7544101E-02 1.236931 at 70iterations 1.7452320E-02 0.6632309 at 80iterations 8.1171468E-03 0.3021393 at 90iterations 3.7798078E-03 0.1421432 at 100iterations 1.7582014E-03 6.1379433E-02 at 110iterations 8.2041899E-04 2.8153896E-02 at 120iterations finished qdiffx linear iterations at : 14:21:01 total time elapsed so far: 8.290000 # loops : 120 mean,max change (kT/e) : 8.2041899E-04 2.8153896E-02 energy calculations done at 8.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.420000 DelPhi exited at 14:21:01 8.421u 0.307s 0:09.06 96.2% 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 Dec 21 2011 at 14:21:01 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 # of charge parameter records: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1953 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.915484 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): -6.227000 30.89700 ymin,ymax (A): -46.66200 7.556000 zmin,zma (A): -54.51700 0.4310000 x,y,z range (A): 37.12400 54.21800 54.94800 scale (grids/A): 2.915484 object centre (A): 12.33500 -19.55300 -27.04300 number of atom coordinates read : 1953 total number of charged atoms : 1820 net assigned charge : 2.681006 assigned positive charge : 286.6021 centred at (gu) : 90.22134 99.71587 89.28667 assigned negative charge : -283.9213 centred at (gu) : 89.69976 100.4032 89.69630 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 140731 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17714 grid for indexing accessible points = 1.400000 m= 72725 mr = 100900 m= 27306 mr = 59975 m= 6728 mr = 22441 m= 992 mr = 5174 m= 60 mr = 713 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 822 time to turn everything in is 0.8300000 number of dielectric boundary points 59309 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 14560 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) : 1.943656 object centre at (A) : 12.33500 -19.55300 -27.04300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9983446E-02 0.8740040 midg,1,midg; midg,igrid,midg 0.4064451 -0.2886665 1,midg,midg; igrid,midg,midg -3.9452728E-02 3.3713780E-02 gauss-seidel spectral radius is 0.9992439 estimated iterations to convergence 287 setup time was (sec) 1.100000 now iterating at: 14:21:03 rms-change max change #iterations 8.645290 390.1042 at 10iterations 4.972305 128.7183 at 20iterations 2.847718 55.34473 at 30iterations 1.630264 37.50767 at 40iterations 0.9288208 19.08857 at 50iterations 0.5305354 10.35282 at 60iterations 0.3030267 6.262075 at 70iterations 0.1723631 3.441391 at 80iterations 9.8301932E-02 1.857362 at 90iterations 5.6001835E-02 1.091640 at 100iterations 3.1858269E-02 0.6379814 at 110iterations 1.8217800E-02 0.3471737 at 120iterations 1.0348880E-02 0.2027988 at 130iterations 5.9010535E-03 0.1188736 at 140iterations 3.3743565E-03 7.5112343E-02 at 150iterations 1.9149210E-03 3.9094448E-02 at 160iterations 1.0898768E-03 2.0640135E-02 at 170iterations 6.2282244E-04 1.1350632E-02 at 180iterations finished qdiffx linear iterations at : 14:21:15 total time elapsed so far: 13.41000 # loops : 180 mean,max change (kT/e) : 6.2282244E-04 1.1350632E-02 energy calculations done at 13.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.54000 DelPhi exited at 14:21:17 13.546u 0.315s 0:15.31 90.4% 0+0k 0+0io 0pf+0w