Mon Oct 10 09:09:36 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 Mon Oct 10 2011 at 09:09:36 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 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: 0.5799556 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): -34.81800 9.911000 ymin,ymax (A): 0.3140000 42.19600 zmin,zma (A): -1.555000 59.82900 x,y,z range (A): 44.72900 41.88200 61.38400 scale (grids/A): 0.5799556 object centre (A): -12.45350 21.25500 29.13700 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 3.000004 assigned positive charge : 290.3540 centred at (gu) : 90.43886 89.40638 89.28096 assigned negative charge : -287.3542 centred at (gu) : 90.36295 89.53800 89.30087 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4379 nv = 96 ne = 84 npr = 40126 no. pairs analyzed = 40126 no. exposed pairs = 2497 no. arc points = 17362 no. surface atoms = 853 nbur = 1105 mkacc time = 6.0000002E-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 = 1.484000 m= 172 mr = 2319 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 6.0000002E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2225 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1769 ## 220 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 5433 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0841045E-09 3.0163883E-10 midg,1,midg; midg,igrid,midg 2.8497327E-09 -1.0935152E-09 1,midg,midg; igrid,midg,midg -4.0461573E-10 1.8896169E-09 gauss-seidel spectral radius is 0.9845688 estimated iterations to convergence 66 setup time was (sec) 0.3400000 now iterating at: 09:09:36 rms-change max change #iterations 7.8380696E-02 12.69063 at 10iterations 6.1503421E-03 1.048204 at 20iterations 4.6932974E-04 7.9566956E-02 at 30iterations 3.6820184E-05 7.3432922E-03 at 40iterations 2.8023110E-06 5.7983398E-04 at 50iterations finished qdiffx linear iterations at : 09:09:39 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 2.8023110E-06 5.7983398E-04 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 09:09:40 3.326u 0.185s 0:03.80 92.1% 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 Mon Oct 10 2011 at 09:09:40 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 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: 1.739867 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): -34.81800 9.911000 ymin,ymax (A): 0.3140000 42.19600 zmin,zma (A): -1.555000 59.82900 x,y,z range (A): 44.72900 41.88200 61.38400 scale (grids/A): 1.739867 object centre (A): -12.45350 21.25500 29.13700 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 3.000004 assigned positive charge : 290.3540 centred at (gu) : 91.31648 88.21916 87.84303 assigned negative charge : -287.3542 centred at (gu) : 91.08888 88.61407 87.90279 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 47380 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17362 grid for indexing accessible points = 1.400000 m= 15913 mr = 31943 m= 1788 mr = 11562 m= 72 mr = 944 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 20687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 173 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 14151 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) : 0.5799556 object centre at (A) : -12.45350 21.25500 29.13700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2314860E-02 1.4321290E-02 midg,1,midg; midg,igrid,midg 1.4983526E-03 -5.1311837E-03 1,midg,midg; igrid,midg,midg -1.8785400E-03 2.4785646E-04 gauss-seidel spectral radius is 0.9982860 estimated iterations to convergence 192 setup time was (sec) 0.4600000 now iterating at: 09:09:40 rms-change max change #iterations 2.988364 160.9985 at 10iterations 1.267492 53.64777 at 20iterations 0.5439891 22.31034 at 30iterations 0.2316023 9.704918 at 40iterations 9.8667420E-02 4.000216 at 50iterations 4.2336036E-02 1.748331 at 60iterations 1.8037625E-02 0.7529330 at 70iterations 7.6919319E-03 0.2906036 at 80iterations 3.2733185E-03 0.1316671 at 90iterations 1.4110608E-03 5.7809353E-02 at 100iterations 6.0166657E-04 2.4155617E-02 at 110iterations 2.5713735E-04 9.6015930E-03 at 120iterations finished qdiffx linear iterations at : 09:09:47 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 2.5713735E-04 9.6015930E-03 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 09:09:48 7.530u 0.194s 0:08.00 96.5% 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 Mon Oct 10 2011 at 09:09:48 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 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: 2.609801 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): -34.81800 9.911000 ymin,ymax (A): 0.3140000 42.19600 zmin,zma (A): -1.555000 59.82900 x,y,z range (A): 44.72900 41.88200 61.38400 scale (grids/A): 2.609801 object centre (A): -12.45350 21.25500 29.13700 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 3.000004 assigned positive charge : 290.3540 centred at (gu) : 91.97472 87.32876 86.76463 assigned negative charge : -287.3542 centred at (gu) : 91.63349 87.92106 86.85418 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 109415 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17362 grid for indexing accessible points = 1.400000 m= 53246 mr = 77487 m= 17084 mr = 43170 m= 2920 mr = 13579 m= 284 mr = 1982 m= 14 mr = 152 m= 0 mr = 8 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 46585 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 14604 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) : 1.739867 object centre at (A) : -12.45350 21.25500 29.13700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1053899 5.9884388E-02 midg,1,midg; midg,igrid,midg -1.1431983E-02 -7.1488775E-02 1,midg,midg; igrid,midg,midg -4.1592810E-02 -3.3016939E-02 gauss-seidel spectral radius is 0.9991359 estimated iterations to convergence 269 setup time was (sec) 0.8200000 now iterating at: 09:09:49 rms-change max change #iterations 7.415643 246.5048 at 10iterations 4.140913 109.7042 at 20iterations 2.293573 59.26201 at 30iterations 1.265665 32.96334 at 40iterations 0.7006339 19.22150 at 50iterations 0.3838348 9.403229 at 60iterations 0.2115997 4.889733 at 70iterations 0.1161440 2.683548 at 80iterations 6.3804448E-02 1.725893 at 90iterations 3.4904737E-02 0.8347285 at 100iterations 1.9215189E-02 0.4423542 at 110iterations 1.0524773E-02 0.2435837 at 120iterations 5.7905326E-03 0.1262255 at 130iterations 3.1667228E-03 7.7984810E-02 at 140iterations 1.7364669E-03 3.7098408E-02 at 150iterations 9.5129141E-04 2.2475481E-02 at 160iterations 5.2160805E-04 1.2893677E-02 at 170iterations 2.8648425E-04 7.2722435E-03 at 180iterations finished qdiffx linear iterations at : 09:10:00 total time elapsed so far: 11.67000 # loops : 180 mean,max change (kT/e) : 2.8648425E-04 7.2722435E-03 energy calculations done at 11.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.79000 DelPhi exited at 09:10:00 11.793u 0.204s 0:12.31 97.4% 0+0k 0+0io 0pf+0w