Tue Nov 22 14:16:57 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 Tue Nov 22 2011 at 14:17:02 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 = 1968 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: 0.5889262 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): -35.42800 10.14200 ymin,ymax (A): 1.086000 42.01900 zmin,zma (A): -2.134000 58.31500 x,y,z range (A): 45.57000 40.93300 60.44900 scale (grids/A): 0.5889262 object centre (A): -12.64300 21.55250 28.09050 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 3.000003 assigned positive charge : 288.9261 centred at (gu) : 90.45608 89.43592 89.78689 assigned negative charge : -285.9263 centred at (gu) : 90.38242 89.56873 89.77195 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4599 nv = 96 ne = 84 npr = 40005 no. pairs analyzed = 40005 no. exposed pairs = 2467 no. arc points = 17560 no. surface atoms = 839 nbur = 1129 mkacc time = 7.0000008E-02 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 = 1.456000 m= 214 mr = 2485 m= 0 mr = 25 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2303 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1779 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 5687 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1424354E-10 1.0987123E-09 midg,1,midg; midg,igrid,midg 3.8194106E-09 -1.4733454E-09 1,midg,midg; igrid,midg,midg -4.7953824E-10 2.5053448E-09 gauss-seidel spectral radius is 0.9850324 estimated iterations to convergence 67 setup time was (sec) 0.3800000 now iterating at: 14:17:05 rms-change max change #iterations 8.2072280E-02 16.42607 at 10iterations 6.4485585E-03 1.246124 at 20iterations 5.2489334E-04 0.1096802 at 30iterations 4.2258569E-05 9.3612671E-03 at 40iterations 3.5002486E-06 6.1035156E-04 at 50iterations finished qdiffx linear iterations at : 14:17:15 total time elapsed so far: 3.610000 # loops : 50 mean,max change (kT/e) : 3.5002486E-06 6.1035156E-04 energy calculations done at 3.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.750000 DelPhi exited at 14:17:16 3.753u 0.223s 0:15.69 25.3% 0+0k 0+0io 3pf+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 Tue Nov 22 2011 at 14:17:22 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 = 1968 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: 1.766779 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): -35.42800 10.14200 ymin,ymax (A): 1.086000 42.01900 zmin,zma (A): -2.134000 58.31500 x,y,z range (A): 45.57000 40.93300 60.44900 scale (grids/A): 1.766779 object centre (A): -12.64300 21.55250 28.09050 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 3.000003 assigned positive charge : 288.9261 centred at (gu) : 91.36854 88.30773 89.36073 assigned negative charge : -285.9263 centred at (gu) : 91.14752 88.70627 89.31595 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 49958 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17560 grid for indexing accessible points = 1.400000 m= 17457 mr = 33927 m= 2163 mr = 12909 m= 98 mr = 1284 m= 0 mr = 34 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 21522 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 14292 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) : 0.5889262 object centre at (A) : -12.64300 21.55250 28.09050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7077029E-02 2.2443654E-02 midg,1,midg; midg,igrid,midg 1.4049580E-03 -8.3111487E-03 1,midg,midg; igrid,midg,midg -9.2639937E-04 -1.4388565E-03 gauss-seidel spectral radius is 0.9983408 estimated iterations to convergence 195 setup time was (sec) 0.5000000 now iterating at: 14:17:27 rms-change max change #iterations 3.077552 147.8424 at 10iterations 1.324962 66.27341 at 20iterations 0.5778549 23.40338 at 30iterations 0.2498528 10.32539 at 40iterations 0.1076807 4.232002 at 50iterations 4.6646819E-02 1.900790 at 60iterations 2.0254195E-02 0.7369828 at 70iterations 8.7925494E-03 0.3412476 at 80iterations 3.7927465E-03 0.1399460 at 90iterations 1.6428989E-03 6.2276840E-02 at 100iterations 7.1372942E-04 3.0253410E-02 at 110iterations 3.0898722E-04 1.0765076E-02 at 120iterations finished qdiffx linear iterations at : 14:17:50 total time elapsed so far: 8.330000 # loops : 120 mean,max change (kT/e) : 3.0898722E-04 1.0765076E-02 energy calculations done at 8.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.460000 DelPhi exited at 14:17:52 8.463u 0.252s 0:29.90 29.1% 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 Tue Nov 22 2011 at 14:17:54 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 = 1968 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: 2.650168 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): -35.42800 10.14200 ymin,ymax (A): 1.086000 42.01900 zmin,zma (A): -2.134000 58.31500 x,y,z range (A): 45.57000 40.93300 60.44900 scale (grids/A): 2.650168 object centre (A): -12.64300 21.55250 28.09050 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 3.000003 assigned positive charge : 288.9261 centred at (gu) : 92.05283 87.46152 89.04102 assigned negative charge : -285.9263 centred at (gu) : 91.72125 88.05953 88.97401 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 115681 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17560 grid for indexing accessible points = 1.400000 m= 57383 mr = 82424 m= 19369 mr = 46972 m= 3892 mr = 15574 m= 431 mr = 2859 m= 19 mr = 303 m= 0 mr = 7 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 48636 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 14685 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) : 1.766779 object centre at (A) : -12.64300 21.55250 28.09050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2468068 0.1432736 midg,1,midg; midg,igrid,midg -1.3480107E-02 -0.1124253 1,midg,midg; igrid,midg,midg -2.4053084E-02 -5.6670293E-02 gauss-seidel spectral radius is 0.9991556 estimated iterations to convergence 272 setup time was (sec) 0.9400000 now iterating at: 14:18:00 rms-change max change #iterations 7.472318 280.9561 at 10iterations 4.187683 115.0989 at 20iterations 2.340232 68.68324 at 30iterations 1.300109 28.81927 at 40iterations 0.7200372 16.07911 at 50iterations 0.4000659 8.944387 at 60iterations 0.2205887 4.925694 at 70iterations 0.1218462 2.786759 at 80iterations 6.7522816E-02 1.677788 at 90iterations 3.7259657E-02 0.8212128 at 100iterations 2.0584280E-02 0.4509931 at 110iterations 1.1373936E-02 0.2568636 at 120iterations 6.2794518E-03 0.1477360 at 130iterations 3.4723871E-03 8.0964088E-02 at 140iterations 1.9114028E-03 4.2228699E-02 at 150iterations 1.0563423E-03 2.3010254E-02 at 160iterations 5.8385951E-04 1.2855530E-02 at 170iterations 3.2128085E-04 7.3241889E-03 at 180iterations finished qdiffx linear iterations at : 14:18:36 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 3.2128085E-04 7.3241889E-03 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.28000 DelPhi exited at 14:18:38 13.286u 0.264s 0:44.59 30.3% 0+0k 0+0io 0pf+0w