Sun Oct 9 11:49:08 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 11:49:08 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 = 2649 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6543155 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): -4.835000 47.66600 ymin,ymax (A): 8.686001 59.71300 zmin,zma (A): 5.271000 59.67900 x,y,z range (A): 52.50100 51.02700 54.40800 scale (grids/A): 0.6543155 object centre (A): 21.41550 34.19950 32.47500 number of atom coordinates read : 2649 total number of charged atoms : 2571 net assigned charge : 2.500009 assigned positive charge : 394.5372 centred at (gu) : 90.53690 90.12540 91.27537 assigned negative charge : -392.0387 centred at (gu) : 90.61157 90.10708 91.20329 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8106 nv = 96 ne = 84 npr = 50488 no. pairs analyzed = 50488 no. exposed pairs = 3767 no. arc points = 26852 no. surface atoms = 1254 nbur = 1395 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 496 mr = 4051 m= 4 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 4472 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2568 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9421 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4121814E-09 2.3142796E-08 midg,1,midg; midg,igrid,midg 2.1221442E-09 8.7101801E-09 1,midg,midg; igrid,midg,midg 1.6171866E-08 -8.6059249E-09 gauss-seidel spectral radius is 0.9879226 estimated iterations to convergence 74 setup time was (sec) 0.6300000 now iterating at: 11:49:09 rms-change max change #iterations 0.1586466 26.56712 at 10iterations 1.6393892E-02 2.129791 at 20iterations 1.7001944E-03 0.2140722 at 30iterations 1.7640994E-04 2.6511669E-02 at 40iterations 1.8849927E-05 2.5386810E-03 at 50iterations finished qdiffx linear iterations at : 11:49:12 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 1.8849927E-05 2.5386810E-03 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 11:49:13 4.079u 0.255s 0:04.64 93.1% 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 Sun Oct 9 2011 at 11:49:13 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 = 2649 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.962947 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): -4.835000 47.66600 ymin,ymax (A): 8.686001 59.71300 zmin,zma (A): 5.271000 59.67900 x,y,z range (A): 52.50100 51.02700 54.40800 scale (grids/A): 1.962947 object centre (A): 21.41550 34.19950 32.47500 number of atom coordinates read : 2649 total number of charged atoms : 2571 net assigned charge : 2.500009 assigned positive charge : 394.5372 centred at (gu) : 91.60976 90.37545 93.82515 assigned negative charge : -392.0387 centred at (gu) : 91.83442 90.32108 93.60957 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 86091 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26852 grid for indexing accessible points = 1.400000 m= 31946 mr = 56898 m= 6213 mr = 22525 m= 500 mr = 3911 m= 4 mr = 211 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 598 time to turn everything in is 0.7800000 number of dielectric boundary points 41209 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 20331 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) : 0.6543155 object centre at (A) : 21.41550 34.19950 32.47500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.2033463E-03 3.0743167E-02 midg,1,midg; midg,igrid,midg 2.6900848E-04 2.5390517E-02 1,midg,midg; igrid,midg,midg -1.0572034E-03 -4.8255012E-03 gauss-seidel spectral radius is 0.9987504 estimated iterations to convergence 224 setup time was (sec) 1.070000 now iterating at: 11:49:14 rms-change max change #iterations 4.535610 182.4647 at 10iterations 2.193933 75.49783 at 20iterations 1.055697 31.58232 at 30iterations 0.5114070 14.80951 at 40iterations 0.2468738 6.935417 at 50iterations 0.1191068 3.716473 at 60iterations 5.7700742E-02 1.726548 at 70iterations 2.7848262E-02 0.9252372 at 80iterations 1.3514024E-02 0.3917021 at 90iterations 6.5336814E-03 0.2165141 at 100iterations 3.1549081E-03 9.8020554E-02 at 110iterations 1.5285269E-03 4.7790527E-02 at 120iterations finished qdiffx linear iterations at : 11:49:23 total time elapsed so far: 9.490000 # loops : 120 mean,max change (kT/e) : 1.5285269E-03 4.7790527E-02 energy calculations done at 9.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.670000 DelPhi exited at 11:49:23 9.675u 0.302s 0:10.23 97.4% 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 11:49:23 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 = 2649 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.944420 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): -4.835000 47.66600 ymin,ymax (A): 8.686001 59.71300 zmin,zma (A): 5.271000 59.67900 x,y,z range (A): 52.50100 51.02700 54.40800 scale (grids/A): 2.944420 object centre (A): 21.41550 34.19950 32.47500 number of atom coordinates read : 2649 total number of charged atoms : 2571 net assigned charge : 2.500009 assigned positive charge : 394.5372 centred at (gu) : 92.41467 90.56312 95.73743 assigned negative charge : -392.0387 centred at (gu) : 92.75163 90.48167 95.41441 start vw surface at 0.1600000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 198669 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26852 grid for indexing accessible points = 1.400000 m= 99720 mr = 138550 m= 39735 mr = 79029 m= 11535 mr = 31224 m= 2174 mr = 8550 m= 177 mr = 1526 m= 5 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 1.270000 no. cavity mid-points inaccessible to solvent = 2040 time to turn everything in is 2.030000 number of dielectric boundary points 93054 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.190000 number of grid points assigned charge 20568 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) : 1.962947 object centre at (A) : 21.41550 34.19950 32.47500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6315971E-02 0.3950379 midg,1,midg; midg,igrid,midg 2.8578121E-02 0.2623804 1,midg,midg; igrid,midg,midg -9.1196619E-02 0.2148622 gauss-seidel spectral radius is 0.9993170 estimated iterations to convergence 302 setup time was (sec) 2.360000 now iterating at: 11:49:26 rms-change max change #iterations 10.79588 558.5159 at 10iterations 6.561037 162.9958 at 20iterations 3.963112 85.81268 at 30iterations 2.385229 50.59399 at 40iterations 1.426418 30.65244 at 50iterations 0.8512242 24.13974 at 60iterations 0.5053222 9.388639 at 70iterations 0.3002788 5.839523 at 80iterations 0.1777761 3.180241 at 90iterations 0.1048578 1.877686 at 100iterations 6.1849836E-02 1.156271 at 110iterations 3.6535244E-02 0.7255056 at 120iterations 2.1541240E-02 0.3726385 at 130iterations 1.2683944E-02 0.2313766 at 140iterations 7.4688625E-03 0.1364012 at 150iterations 4.4045779E-03 7.4867249E-02 at 160iterations 2.5921473E-03 4.7649622E-02 at 170iterations 1.5291858E-03 2.6577473E-02 at 180iterations finished qdiffx linear iterations at : 11:49:40 total time elapsed so far: 16.53000 # loops : 180 mean,max change (kT/e) : 1.5291858E-03 2.6577473E-02 energy calculations done at 16.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.71000 DelPhi exited at 11:49:40 16.708u 0.308s 0:17.33 98.0% 0+0k 0+0io 0pf+0w