Sun Oct 9 12:20:17 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 Sun Oct 9 2011 at 12:20:17 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 = 2416 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6737958 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): -14.27500 38.56000 ymin,ymax (A): -0.1560000 44.71900 zmin,zma (A): -7.104000 43.75900 x,y,z range (A): 52.83500 44.87500 50.86300 scale (grids/A): 0.6737958 object centre (A): 12.14250 22.28150 18.32750 number of atom coordinates read : 2416 total number of charged atoms : 2274 net assigned charge : 3.500024 assigned positive charge : 370.2130 centred at (gu) : 90.66434 91.11787 90.04777 assigned negative charge : -366.7136 centred at (gu) : 90.85495 91.18197 90.01711 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7222 nv = 96 ne = 84 npr = 48222 no. pairs analyzed = 48222 no. exposed pairs = 3128 no. arc points = 21210 no. surface atoms = 1052 nbur = 1364 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 461 mr = 3907 m= 4 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.1800000 number of dielectric boundary points 3699 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2006 ## 178 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8466 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2902376E-09 2.1723581E-08 midg,1,midg; midg,igrid,midg 2.4133760E-08 -4.7379491E-09 1,midg,midg; igrid,midg,midg 5.4761152E-08 -4.3627722E-08 gauss-seidel spectral radius is 0.9885617 estimated iterations to convergence 76 setup time was (sec) 0.3700000 now iterating at: 12:20:17 rms-change max change #iterations 0.1781699 23.89088 at 10iterations 1.9860981E-02 2.811682 at 20iterations 2.6008415E-03 0.3596115 at 30iterations 5.1067508E-04 7.6897860E-02 at 40iterations 1.5720871E-04 2.2165298E-02 at 50iterations finished qdiffx linear iterations at : 12:20:20 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.5720871E-04 2.2165298E-02 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 12:20:21 3.458u 0.209s 0:04.08 89.4% 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 Sun Oct 9 2011 at 12:20:21 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 = 2416 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: 2.021387 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): -14.27500 38.56000 ymin,ymax (A): -0.1560000 44.71900 zmin,zma (A): -7.104000 43.75900 x,y,z range (A): 52.83500 44.87500 50.86300 scale (grids/A): 2.021387 object centre (A): 12.14250 22.28150 18.32750 number of atom coordinates read : 2416 total number of charged atoms : 2274 net assigned charge : 3.500024 assigned positive charge : 370.2130 centred at (gu) : 91.99247 93.35293 90.14301 assigned negative charge : -366.7136 centred at (gu) : 92.56464 93.54566 90.05125 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76545 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21210 grid for indexing accessible points = 1.400000 m= 28791 mr = 52201 m= 5311 mr = 21222 m= 388 mr = 3438 m= 14 mr = 180 m= 2 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 860 time to turn everything in is 0.4100000 number of dielectric boundary points 34007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 17989 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) : 0.6737958 object centre at (A) : 12.14250 22.28150 18.32750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2317247E-02 1.5153875E-02 midg,1,midg; midg,igrid,midg 3.2467302E-02 1.9096481E-03 1,midg,midg; igrid,midg,midg 2.2667028E-02 -4.7221325E-02 gauss-seidel spectral radius is 0.9987666 estimated iterations to convergence 225 setup time was (sec) 0.6600000 now iterating at: 12:20:22 rms-change max change #iterations 4.637097 236.2536 at 10iterations 2.245043 84.12389 at 20iterations 1.088781 34.72728 at 30iterations 0.5313357 16.47905 at 40iterations 0.2575191 8.569992 at 50iterations 0.1252757 3.748669 at 60iterations 6.0848743E-02 1.898254 at 70iterations 2.9808057E-02 0.9250031 at 80iterations 1.4600265E-02 0.4358349 at 90iterations 7.1903705E-03 0.2157273 at 100iterations 3.5971452E-03 0.1119576 at 110iterations 1.8481571E-03 5.8319092E-02 at 120iterations finished qdiffx linear iterations at : 12:20:29 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 1.8481571E-03 5.8319092E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 12:20:30 7.981u 0.209s 0:08.58 95.3% 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 Sun Oct 9 2011 at 12:20:30 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 = 2416 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.032081 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): -14.27500 38.56000 ymin,ymax (A): -0.1560000 44.71900 zmin,zma (A): -7.104000 43.75900 x,y,z range (A): 52.83500 44.87500 50.86300 scale (grids/A): 3.032081 object centre (A): 12.14250 22.28150 18.32750 number of atom coordinates read : 2416 total number of charged atoms : 2274 net assigned charge : 3.500024 assigned positive charge : 370.2130 centred at (gu) : 92.98843 95.02924 90.21427 assigned negative charge : -366.7136 centred at (gu) : 93.84693 95.31856 90.07682 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 176449 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21210 grid for indexing accessible points = 1.400000 m= 91330 mr = 126613 m= 35538 mr = 74263 m= 9878 mr = 28707 m= 1768 mr = 7577 m= 148 mr = 1242 m= 4 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 2947 time to turn everything in is 1.050000 number of dielectric boundary points 76634 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 18191 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) : 2.021387 object centre at (A) : 12.14250 22.28150 18.32750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2002113 7.8113735E-02 midg,1,midg; midg,igrid,midg 0.2923293 -0.1021476 1,midg,midg; igrid,midg,midg 0.3600558 -0.4388753 gauss-seidel spectral radius is 0.9992864 estimated iterations to convergence 295 setup time was (sec) 1.300000 now iterating at: 12:20:31 rms-change max change #iterations 10.65162 370.9242 at 10iterations 6.325553 147.7775 at 20iterations 3.754388 69.93839 at 30iterations 2.207975 42.22194 at 40iterations 1.296611 23.14431 at 50iterations 0.7622451 14.45662 at 60iterations 0.4454657 8.447526 at 70iterations 0.2605971 4.488161 at 80iterations 0.1522768 2.878555 at 90iterations 8.8901579E-02 1.592430 at 100iterations 5.2005120E-02 0.8858147 at 110iterations 3.0544104E-02 0.5096588 at 120iterations 1.7920919E-02 0.3166695 at 130iterations 1.0634325E-02 0.2121773 at 140iterations 6.4021382E-03 0.1372490 at 150iterations 3.9692232E-03 7.9200745E-02 at 160iterations 2.5682559E-03 5.5637360E-02 at 170iterations 1.7571740E-03 3.6844254E-02 at 180iterations finished qdiffx linear iterations at : 12:20:43 total time elapsed so far: 12.69000 # loops : 180 mean,max change (kT/e) : 1.7571740E-03 3.6844254E-02 energy calculations done at 12.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.83000 DelPhi exited at 12:20:43 12.831u 0.217s 0:13.38 97.4% 0+0k 0+0io 0pf+0w