Sat Oct 15 11:47:32 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 Sat Oct 15 2011 at 11:47:32 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2227 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6518952 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): -15.51900 27.88900 ymin,ymax (A): -11.77800 41.80300 zmin,zma (A): 0.3530000 54.96300 x,y,z range (A): 43.40800 53.58100 54.61000 scale (grids/A): 0.6518952 object centre (A): 6.185000 15.01250 27.65800 number of atom coordinates read : 2227 total number of charged atoms : 2093 net assigned charge : 11.00003 assigned positive charge : 326.4138 centred at (gu) : 88.60272 91.32571 88.81231 assigned negative charge : -315.4143 centred at (gu) : 88.70430 91.33496 88.81078 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6554 nv = 96 ne = 84 npr = 44416 no. pairs analyzed = 44416 no. exposed pairs = 3041 no. arc points = 21683 no. surface atoms = 1010 nbur = 1217 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 413 mr = 3362 m= 4 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2133 ## 206 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7676 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7909763E-08 1.7553576E-08 midg,1,midg; midg,igrid,midg 1.7829564E-08 2.7378132E-08 1,midg,midg; igrid,midg,midg 4.7037041E-08 6.7995636E-09 gauss-seidel spectral radius is 0.9877825 estimated iterations to convergence 74 setup time was (sec) 0.4200000 now iterating at: 11:47:32 rms-change max change #iterations 0.1469990 23.34030 at 10iterations 1.5115795E-02 2.438620 at 20iterations 1.5625436E-03 0.2046413 at 30iterations 1.6955692E-04 2.4528503E-02 at 40iterations 2.2863676E-05 3.4294128E-03 at 50iterations finished qdiffx linear iterations at : 11:47:36 total time elapsed so far: 3.610000 # loops : 50 mean,max change (kT/e) : 2.2863676E-05 3.4294128E-03 energy calculations done at 3.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 11:47:36 3.745u 0.253s 0:04.52 88.2% 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 Sat Oct 15 2011 at 11:47:36 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2227 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.955686 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): -15.51900 27.88900 ymin,ymax (A): -11.77800 41.80300 zmin,zma (A): 0.3530000 54.96300 x,y,z range (A): 43.40800 53.58100 54.61000 scale (grids/A): 1.955686 object centre (A): 6.185000 15.01250 27.65800 number of atom coordinates read : 2227 total number of charged atoms : 2093 net assigned charge : 11.00003 assigned positive charge : 326.4138 centred at (gu) : 85.80802 93.97709 86.43678 assigned negative charge : -315.4143 centred at (gu) : 86.11295 94.00498 86.43256 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69922 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21683 grid for indexing accessible points = 1.400000 m= 25598 mr = 46491 m= 4636 mr = 18194 m= 345 mr = 2779 m= 8 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 32900 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 16523 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) : 0.6518952 object centre at (A) : 6.185000 15.01250 27.65800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5648407E-02 3.8831007E-02 midg,1,midg; midg,igrid,midg 5.0948035E-02 2.6735848E-02 1,midg,midg; igrid,midg,midg 3.3346273E-02 -2.9891583E-03 gauss-seidel spectral radius is 0.9986747 estimated iterations to convergence 218 setup time was (sec) 0.6100000 now iterating at: 11:47:37 rms-change max change #iterations 4.035101 181.9048 at 10iterations 1.906605 65.51421 at 20iterations 0.8996429 33.23186 at 30iterations 0.4272625 13.93709 at 40iterations 0.2013712 6.672441 at 50iterations 9.5249429E-02 3.274541 at 60iterations 4.5062657E-02 1.522278 at 70iterations 2.1341927E-02 0.7427759 at 80iterations 1.0100447E-02 0.4057980 at 90iterations 4.7583641E-03 0.1562653 at 100iterations 2.2590796E-03 8.0015182E-02 at 110iterations 1.0778384E-03 3.7117004E-02 at 120iterations finished qdiffx linear iterations at : 11:47:48 total time elapsed so far: 8.320000 # loops : 120 mean,max change (kT/e) : 1.0778384E-03 3.7117004E-02 energy calculations done at 8.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.450000 DelPhi exited at 11:47:48 8.448u 0.267s 0:12.04 72.2% 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 Sat Oct 15 2011 at 11:47:48 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2227 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: 2.933529 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): -15.51900 27.88900 ymin,ymax (A): -11.77800 41.80300 zmin,zma (A): 0.3530000 54.96300 x,y,z range (A): 43.40800 53.58100 54.61000 scale (grids/A): 2.933529 object centre (A): 6.185000 15.01250 27.65800 number of atom coordinates read : 2227 total number of charged atoms : 2093 net assigned charge : 11.00003 assigned positive charge : 326.4138 centred at (gu) : 83.71209 95.96544 84.65521 assigned negative charge : -315.4143 centred at (gu) : 84.16953 96.00756 84.64896 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 161355 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21683 grid for indexing accessible points = 1.400000 m= 80911 mr = 112805 m= 30915 mr = 64670 m= 8410 mr = 24160 m= 1482 mr = 6236 m= 140 mr = 961 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9600000 number of dielectric boundary points 74325 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 16744 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) : 1.955686 object centre at (A) : 6.185000 15.01250 27.65800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6246428 0.4231187 midg,1,midg; midg,igrid,midg 0.7004240 0.3066477 1,midg,midg; igrid,midg,midg 0.2902644 -3.2562569E-02 gauss-seidel spectral radius is 0.9992778 estimated iterations to convergence 294 setup time was (sec) 1.250000 now iterating at: 11:47:50 rms-change max change #iterations 9.634170 449.5744 at 10iterations 5.721069 153.2641 at 20iterations 3.370297 78.67676 at 30iterations 1.979826 48.11617 at 40iterations 1.160483 26.05644 at 50iterations 0.6777967 12.76374 at 60iterations 0.3953258 7.594133 at 70iterations 0.2293196 4.583753 at 80iterations 0.1333203 2.757624 at 90iterations 7.7592358E-02 1.514210 at 100iterations 4.4936843E-02 0.8644104 at 110iterations 2.6098972E-02 0.5313187 at 120iterations 1.5110466E-02 0.2904649 at 130iterations 8.7606721E-03 0.1742191 at 140iterations 5.0877533E-03 9.6168518E-02 at 150iterations 2.9465489E-03 5.1239014E-02 at 160iterations 1.7142961E-03 3.0626297E-02 at 170iterations 9.9930586E-04 1.8562317E-02 at 180iterations finished qdiffx linear iterations at : 11:48:06 total time elapsed so far: 13.93000 # loops : 180 mean,max change (kT/e) : 9.9930586E-04 1.8562317E-02 energy calculations done at 13.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.07000 DelPhi exited at 11:48:06 14.072u 0.286s 0:17.99 79.7% 0+0k 0+0io 0pf+0w