Mon Oct 10 00:05:49 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 Mon Oct 10 2011 at 00:05:49 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 = 3098 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: 0.6197556 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): -34.65600 19.53100 ymin,ymax (A): -13.56600 37.68000 zmin,zma (A): -14.78100 42.66100 x,y,z range (A): 54.18700 51.24600 57.44200 scale (grids/A): 0.6197556 object centre (A): -7.562501 12.05700 13.94000 number of atom coordinates read : 3098 total number of charged atoms : 2955 net assigned charge : 1.500007 assigned positive charge : 466.7739 centred at (gu) : 90.93818 90.44456 91.27579 assigned negative charge : -465.2753 centred at (gu) : 90.89956 90.34722 91.18716 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7907 nv = 96 ne = 84 npr = 61573 no. pairs analyzed = 61573 no. exposed pairs = 4054 no. arc points = 28864 no. surface atoms = 1350 nbur = 1748 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 4129 m= 0 mr = 40 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.2300000 number of dielectric boundary points 4135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2823 ## 305 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9792 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5279624E-09 1.0602271E-08 midg,1,midg; midg,igrid,midg -6.0939991E-09 9.5367589E-09 1,midg,midg; igrid,midg,midg -1.6360053E-09 5.0122284E-09 gauss-seidel spectral radius is 0.9865659 estimated iterations to convergence 71 setup time was (sec) 0.4200000 now iterating at: 00:05:50 rms-change max change #iterations 0.1349714 21.15566 at 10iterations 1.2306489E-02 1.740883 at 20iterations 1.1347883E-03 0.1632652 at 30iterations 1.0588729E-04 1.5018463E-02 at 40iterations 9.9767367E-06 1.4017224E-03 at 50iterations finished qdiffx linear iterations at : 00:05:53 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 9.9767367E-06 1.4017224E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 00:05:53 3.468u 0.172s 0:03.90 93.0% 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 00:05:53 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 = 3098 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: 1.859267 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): -34.65600 19.53100 ymin,ymax (A): -13.56600 37.68000 zmin,zma (A): -14.78100 42.66100 x,y,z range (A): 54.18700 51.24600 57.44200 scale (grids/A): 1.859267 object centre (A): -7.562501 12.05700 13.94000 number of atom coordinates read : 3098 total number of charged atoms : 2955 net assigned charge : 1.500007 assigned positive charge : 466.7739 centred at (gu) : 92.81377 91.33276 93.82664 assigned negative charge : -465.2753 centred at (gu) : 92.69848 91.04137 93.56117 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 86517 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28864 grid for indexing accessible points = 1.400000 m= 28483 mr = 58689 m= 3749 mr = 19977 m= 184 mr = 2034 m= 3 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1529 time to turn everything in is 0.4300000 number of dielectric boundary points 38197 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 223 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 23144 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) : 0.6197556 object centre at (A) : -7.562501 12.05700 13.94000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3292527E-03 9.5218811E-03 midg,1,midg; midg,igrid,midg -8.2864696E-03 1.3432782E-02 1,midg,midg; igrid,midg,midg -1.7974969E-02 3.4630797E-03 gauss-seidel spectral radius is 0.9986305 estimated iterations to convergence 214 setup time was (sec) 0.6500000 now iterating at: 00:05:54 rms-change max change #iterations 4.480801 179.8188 at 10iterations 2.082399 65.15100 at 20iterations 0.9703705 30.80247 at 30iterations 0.4538364 13.80078 at 40iterations 0.2134506 7.145151 at 50iterations 9.8966457E-02 3.071755 at 60iterations 4.6529680E-02 1.512169 at 70iterations 2.1732891E-02 0.6779184 at 80iterations 1.0116186E-02 0.3231735 at 90iterations 4.7385376E-03 0.1543145 at 100iterations 2.2217717E-03 7.0104599E-02 at 110iterations 1.0340039E-03 2.9120207E-02 at 120iterations finished qdiffx linear iterations at : 00:06:01 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 1.0340039E-03 2.9120207E-02 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 00:06:02 8.024u 0.177s 0:08.46 96.8% 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 00:06:02 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 = 3098 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.788900 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): -34.65600 19.53100 ymin,ymax (A): -13.56600 37.68000 zmin,zma (A): -14.78100 42.66100 x,y,z range (A): 54.18700 51.24600 57.44200 scale (grids/A): 2.788900 object centre (A): -7.562501 12.05700 13.94000 number of atom coordinates read : 3098 total number of charged atoms : 2955 net assigned charge : 1.500007 assigned positive charge : 466.7739 centred at (gu) : 94.22038 91.99903 95.73967 assigned negative charge : -465.2753 centred at (gu) : 94.04763 91.56210 95.34149 start vw surface at 0.1000000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 200485 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28864 grid for indexing accessible points = 1.400000 m= 94855 mr = 142918 m= 30740 mr = 75857 m= 6368 mr = 23568 m= 733 mr = 4333 m= 34 mr = 411 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 5357 time to turn everything in is 1.060000 number of dielectric boundary points 86126 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 23638 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) : 1.859267 object centre at (A) : -7.562501 12.05700 13.94000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1056736 -7.9057412E-03 midg,1,midg; midg,igrid,midg -9.5870588E-03 -6.0780339E-02 1,midg,midg; igrid,midg,midg -0.2857521 -3.4037482E-02 gauss-seidel spectral radius is 0.9992791 estimated iterations to convergence 294 setup time was (sec) 1.310000 now iterating at: 00:06:03 rms-change max change #iterations 10.76069 329.9633 at 10iterations 6.448590 137.4324 at 20iterations 3.829795 85.82810 at 30iterations 2.256202 44.39763 at 40iterations 1.327641 35.22636 at 50iterations 0.7762851 14.14465 at 60iterations 0.4534914 8.846970 at 70iterations 0.2642313 5.257874 at 80iterations 0.1535051 2.860851 at 90iterations 8.9308478E-02 1.469593 at 100iterations 5.1872753E-02 0.9325655 at 110iterations 3.0076452E-02 0.5505285 at 120iterations 1.7473958E-02 0.3318844 at 130iterations 1.0111764E-02 0.1919785 at 140iterations 5.8620139E-03 0.1074800 at 150iterations 3.3920375E-03 5.8763504E-02 at 160iterations 1.9657747E-03 3.8974762E-02 at 170iterations 1.1390507E-03 2.0748138E-02 at 180iterations finished qdiffx linear iterations at : 00:06:15 total time elapsed so far: 12.89000 # loops : 180 mean,max change (kT/e) : 1.1390507E-03 2.0748138E-02 energy calculations done at 12.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.02000 DelPhi exited at 00:06:15 13.021u 0.197s 0:13.48 97.9% 0+0k 0+0io 0pf+0w