Wed Dec 21 14:23:03 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+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 Wed Dec 21 2011 at 14:23:04 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6453250 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): -5.525000 35.07100 ymin,ymax (A): -3.494000 47.94500 zmin,zma (A): -24.28900 30.87700 x,y,z range (A): 40.59600 51.43900 55.16600 scale (grids/A): 0.6453250 object centre (A): 14.77300 22.22550 3.294001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 291.8260 centred at (gu) : 90.62553 92.74398 90.24043 assigned negative charge : -289.8262 centred at (gu) : 90.75600 92.92117 90.18597 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5612 nv = 96 ne = 84 npr = 40063 no. pairs analyzed = 40063 no. exposed pairs = 2421 no. arc points = 16837 no. surface atoms = 818 nbur = 1146 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 278 mr = 3214 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 48 time to turn everything in is 0.3300000 number of dielectric boundary points 2631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1715 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 6588 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3617860E-09 9.8902877E-09 midg,1,midg; midg,igrid,midg 1.1945336E-08 -2.5811065E-08 1,midg,midg; igrid,midg,midg 1.4714996E-08 -1.0531011E-08 gauss-seidel spectral radius is 0.9875003 estimated iterations to convergence 73 setup time was (sec) 0.7300000 now iterating at: 14:23:06 rms-change max change #iterations 0.1266790 21.19750 at 10iterations 1.3346616E-02 1.956938 at 20iterations 1.3106529E-03 0.1821480 at 30iterations 1.3298578E-04 2.7524948E-02 at 40iterations 1.3005576E-05 2.0551682E-03 at 50iterations finished qdiffx linear iterations at : 14:23:12 total time elapsed so far: 6.840000 # loops : 50 mean,max change (kT/e) : 1.3005576E-05 2.0551682E-03 energy calculations done at 6.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.070000 DelPhi exited at 14:23:15 7.076u 0.548s 0:11.19 68.0% 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 Wed Dec 21 2011 at 14:23:15 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.935975 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): -5.525000 35.07100 ymin,ymax (A): -3.494000 47.94500 zmin,zma (A): -24.28900 30.87700 x,y,z range (A): 40.59600 51.43900 55.16600 scale (grids/A): 1.935975 object centre (A): 14.77300 22.22550 3.294001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 291.8260 centred at (gu) : 91.87658 98.23199 90.72115 assigned negative charge : -289.8262 centred at (gu) : 92.26802 98.76356 90.55795 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 60226 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16837 grid for indexing accessible points = 1.400000 m= 22602 mr = 42167 m= 3384 mr = 17528 m= 197 mr = 2243 m= 5 mr = 104 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1319 time to turn everything in is 0.6600000 number of dielectric boundary points 24373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 14472 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) : 0.6453250 object centre at (A) : 14.77300 22.22550 3.294001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3872125E-02 1.2709389E-02 midg,1,midg; midg,igrid,midg 3.4358300E-02 -2.0225601E-02 1,midg,midg; igrid,midg,midg 1.0408744E-02 -6.3233734E-03 gauss-seidel spectral radius is 0.9985966 estimated iterations to convergence 212 setup time was (sec) 1.110000 now iterating at: 14:23:17 rms-change max change #iterations 3.744529 197.6852 at 10iterations 1.732177 63.70669 at 20iterations 0.8066170 29.78420 at 30iterations 0.3740753 13.64730 at 40iterations 0.1731456 6.063515 at 50iterations 8.0244340E-02 2.866483 at 60iterations 3.7172303E-02 1.220566 at 70iterations 1.7219838E-02 0.6077192 at 80iterations 7.9843402E-03 0.2759786 at 90iterations 3.7148043E-03 0.1291714 at 100iterations 1.7134221E-03 5.8489084E-02 at 110iterations 7.9607760E-04 2.8133392E-02 at 120iterations finished qdiffx linear iterations at : 14:23:33 total time elapsed so far: 17.06000 # loops : 120 mean,max change (kT/e) : 7.9607760E-04 2.8133392E-02 energy calculations done at 17.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.28000 DelPhi exited at 14:23:34 17.281u 0.637s 0:18.67 95.9% 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 Wed Dec 21 2011 at 14:23:34 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.903963 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): -5.525000 35.07100 ymin,ymax (A): -3.494000 47.94500 zmin,zma (A): -24.28900 30.87700 x,y,z range (A): 40.59600 51.43900 55.16600 scale (grids/A): 2.903963 object centre (A): 14.77300 22.22550 3.294001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 291.8260 centred at (gu) : 92.81481 102.3481 91.08178 assigned negative charge : -289.8262 centred at (gu) : 93.40198 103.1454 90.83695 start vw surface at 0.1400000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 139272 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16837 grid for indexing accessible points = 1.400000 m= 72730 mr = 101727 m= 26685 mr = 61052 m= 5924 mr = 22363 m= 845 mr = 4697 m= 71 mr = 642 m= 0 mr = 42 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 4418 time to turn everything in is 1.650000 number of dielectric boundary points 55004 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 14656 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) : 1.935975 object centre at (A) : 14.77300 22.22550 3.294001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.021410 -4.3982394E-02 midg,1,midg; midg,igrid,midg 0.3816701 -0.2092579 1,midg,midg; igrid,midg,midg 7.1196973E-02 -4.0304355E-02 gauss-seidel spectral radius is 0.9992335 estimated iterations to convergence 285 setup time was (sec) 2.130000 now iterating at: 14:23:37 rms-change max change #iterations 8.729614 360.2914 at 10iterations 5.003690 133.2765 at 20iterations 2.841053 57.44943 at 30iterations 1.612815 33.51957 at 40iterations 0.9172783 19.86838 at 50iterations 0.5206466 10.70650 at 60iterations 0.2954260 5.630718 at 70iterations 0.1679148 3.400482 at 80iterations 9.4988205E-02 1.908398 at 90iterations 5.4002307E-02 1.142419 at 100iterations 3.0626440E-02 0.6696602 at 110iterations 1.7391983E-02 0.3419876 at 120iterations 9.8666679E-03 0.1926270 at 130iterations 5.6033419E-03 0.1156874 at 140iterations 3.1854734E-03 5.9902668E-02 at 150iterations 1.8061673E-03 3.9186478E-02 at 160iterations 1.0279422E-03 2.1209717E-02 at 170iterations 5.8320508E-04 1.2556076E-02 at 180iterations finished qdiffx linear iterations at : 14:24:03 total time elapsed so far: 28.63000 # loops : 180 mean,max change (kT/e) : 5.8320508E-04 1.2556076E-02 energy calculations done at 28.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 28.85000 DelPhi exited at 14:24:04 28.859u 0.733s 0:29.89 98.9% 0+0k 0+0io 0pf+0w