Mon Oct 10 09:09:12 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 09:09:12 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 = 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 : 287.5540 centred at (gu) : 90.42024 89.42611 89.29189 assigned negative charge : -284.5543 centred at (gu) : 90.33904 89.56585 89.31078 start vw surface at 7.0000000E-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 = 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 = 1.484000 m= 172 mr = 2319 m= 2 mr = 9 m= 0 mr = 0 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 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 1.0614735E-09 3.1693032E-10 midg,1,midg; midg,igrid,midg 2.9430274E-09 -1.1855609E-09 1,midg,midg; igrid,midg,midg -4.6546242E-10 1.9508317E-09 gauss-seidel spectral radius is 0.9845688 estimated iterations to convergence 66 setup time was (sec) 0.3400000 now iterating at: 09:09:12 rms-change max change #iterations 7.5497426E-02 12.40062 at 10iterations 5.9031690E-03 1.004309 at 20iterations 4.5350494E-04 7.9015732E-02 at 30iterations 3.5666253E-05 6.9179535E-03 at 40iterations 2.7012452E-06 5.2452087E-04 at 50iterations finished qdiffx linear iterations at : 09:09:15 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 2.7012452E-06 5.2452087E-04 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 09:09:15 3.332u 0.167s 0:03.81 91.6% 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 09:09:15 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: 236 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 : 287.5540 centred at (gu) : 91.26068 88.27842 87.87591 assigned negative charge : -284.5543 centred at (gu) : 91.01722 88.69769 87.93252 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1200000 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 0.2400000 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 0.3200000 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 2.2245171E-02 1.4227824E-02 midg,1,midg; midg,igrid,midg 2.1982656E-03 -5.4285596E-03 1,midg,midg; igrid,midg,midg -2.1357825E-03 4.7245529E-04 gauss-seidel spectral radius is 0.9982860 estimated iterations to convergence 192 setup time was (sec) 0.4600000 now iterating at: 09:09:16 rms-change max change #iterations 2.939466 160.9985 at 10iterations 1.247103 53.63868 at 20iterations 0.5351676 21.77193 at 30iterations 0.2279055 9.632612 at 40iterations 9.7074732E-02 4.199575 at 50iterations 4.1659214E-02 1.715438 at 60iterations 1.7757146E-02 0.6987638 at 70iterations 7.5687277E-03 0.2895508 at 80iterations 3.2196420E-03 0.1258478 at 90iterations 1.3888252E-03 5.7963371E-02 at 100iterations 5.9262925E-04 2.3651123E-02 at 110iterations 2.5299739E-04 9.9582672E-03 at 120iterations finished qdiffx linear iterations at : 09:09:23 total time elapsed so far: 7.340000 # loops : 120 mean,max change (kT/e) : 2.5299739E-04 9.9582672E-03 energy calculations done at 7.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.470000 DelPhi exited at 09:09:24 7.471u 0.193s 0:08.07 94.9% 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 Mon Oct 10 2011 at 09:09:24 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 = 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 : 287.5540 centred at (gu) : 91.89102 87.41764 86.81394 assigned negative charge : -284.5543 centred at (gu) : 91.52598 88.04648 86.89878 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2100000 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 0.1053533 5.8487467E-02 midg,1,midg; midg,igrid,midg -2.2831452E-03 -7.5295702E-02 1,midg,midg; igrid,midg,midg -4.4980761E-02 -3.0357271E-02 gauss-seidel spectral radius is 0.9991359 estimated iterations to convergence 269 setup time was (sec) 0.8300000 now iterating at: 09:09:25 rms-change max change #iterations 7.316464 246.5046 at 10iterations 4.085305 109.6965 at 20iterations 2.263366 60.63788 at 30iterations 1.249569 32.35722 at 40iterations 0.6918748 19.22115 at 50iterations 0.3791790 9.087616 at 60iterations 0.2090148 4.962146 at 70iterations 0.1147560 2.666428 at 80iterations 6.3022867E-02 1.673584 at 90iterations 3.4494318E-02 0.8101966 at 100iterations 1.8990042E-02 0.4335670 at 110iterations 1.0399653E-02 0.2473564 at 120iterations 5.7220613E-03 0.1276753 at 130iterations 3.1300345E-03 7.5617790E-02 at 140iterations 1.7161161E-03 3.7051201E-02 at 150iterations 9.4017829E-04 2.2392273E-02 at 160iterations 5.1567930E-04 1.2847900E-02 at 170iterations 2.8309252E-04 7.3015690E-03 at 180iterations finished qdiffx linear iterations at : 09:09:35 total time elapsed so far: 11.67000 # loops : 180 mean,max change (kT/e) : 2.8309252E-04 7.3015690E-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) 11.81000 DelPhi exited at 09:09:36 11.808u 0.189s 0:12.27 97.6% 0+0k 0+0io 0pf+0w