Sun Oct 9 13:39:54 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 13:39:54 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 = 2359 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6952310 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): -0.2040000 45.88700 ymin,ymax (A): 35.64300 85.92400 zmin,zma (A): -24.13400 27.07200 x,y,z range (A): 46.09100 50.28101 51.20600 scale (grids/A): 0.6952310 object centre (A): 22.84150 60.78350 1.469001 number of atom coordinates read : 2359 total number of charged atoms : 2217 net assigned charge : 1.500017 assigned positive charge : 357.8471 centred at (gu) : 89.80628 89.90121 90.79060 assigned negative charge : -356.3476 centred at (gu) : 89.89753 90.11549 90.72340 start vw surface at 0.1600000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7754 nv = 96 ne = 84 npr = 47325 no. pairs analyzed = 47325 no. exposed pairs = 3015 no. arc points = 21066 no. surface atoms = 1011 nbur = 1348 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 459 mr = 4293 m= 1 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1934 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8680 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6829331E-08 4.4187033E-08 midg,1,midg; midg,igrid,midg 1.0088151E-07 -8.2929525E-08 1,midg,midg; igrid,midg,midg 4.9725973E-08 -2.9105493E-08 gauss-seidel spectral radius is 0.9892514 estimated iterations to convergence 79 setup time was (sec) 0.6200000 now iterating at: 13:39:55 rms-change max change #iterations 0.1980860 30.62633 at 10iterations 2.3889689E-02 3.234818 at 20iterations 3.4701331E-03 0.4848785 at 30iterations 8.1045984E-04 0.1179886 at 40iterations 2.6544678E-04 3.9741516E-02 at 50iterations finished qdiffx linear iterations at : 13:39:59 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 2.6544678E-04 3.9741516E-02 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 13:39:59 4.065u 0.253s 0:04.59 93.8% 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 13:39:59 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 = 2359 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.085693 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): -0.2040000 45.88700 ymin,ymax (A): 35.64300 85.92400 zmin,zma (A): -24.13400 27.07200 x,y,z range (A): 46.09100 50.28101 51.20600 scale (grids/A): 2.085693 object centre (A): 22.84150 60.78350 1.469001 number of atom coordinates read : 2359 total number of charged atoms : 2217 net assigned charge : 1.500017 assigned positive charge : 357.8471 centred at (gu) : 89.41840 89.70342 92.37131 assigned negative charge : -356.3476 centred at (gu) : 89.69241 90.34635 92.16998 start vw surface at 0.1300000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 82790 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21066 grid for indexing accessible points = 1.400000 m= 31461 mr = 57642 m= 5345 mr = 23365 m= 461 mr = 3393 m= 11 mr = 223 m= 0 mr = 4 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 35441 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 102 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 17587 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) : 0.6952310 object centre at (A) : 22.84150 60.78350 1.469001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2969501E-02 2.3713142E-02 midg,1,midg; midg,igrid,midg 9.4046630E-02 -6.1449166E-02 1,midg,midg; igrid,midg,midg -2.4699513E-04 -6.7124534E-03 gauss-seidel spectral radius is 0.9988326 estimated iterations to convergence 232 setup time was (sec) 1.010000 now iterating at: 13:40:00 rms-change max change #iterations 4.838677 216.9330 at 10iterations 2.387216 73.34245 at 20iterations 1.186632 37.44649 at 30iterations 0.5847111 16.46072 at 40iterations 0.2909981 8.375731 at 50iterations 0.1442681 4.677099 at 60iterations 7.1542330E-02 2.198305 at 70iterations 3.5712391E-02 1.099472 at 80iterations 1.7915968E-02 0.5033898 at 90iterations 9.0375124E-03 0.2560997 at 100iterations 4.6057622E-03 0.1400909 at 110iterations 2.4270881E-03 7.2196960E-02 at 120iterations finished qdiffx linear iterations at : 13:40:09 total time elapsed so far: 9.370000 # loops : 120 mean,max change (kT/e) : 2.4270881E-03 7.2196960E-02 energy calculations done at 9.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.540000 DelPhi exited at 13:40:09 9.546u 0.331s 0:10.18 96.9% 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 Sun Oct 9 2011 at 13:40:09 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 = 2359 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.128540 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): -0.2040000 45.88700 ymin,ymax (A): 35.64300 85.92400 zmin,zma (A): -24.13400 27.07200 x,y,z range (A): 46.09100 50.28101 51.20600 scale (grids/A): 3.128540 object centre (A): 22.84150 60.78350 1.469001 number of atom coordinates read : 2359 total number of charged atoms : 2217 net assigned charge : 1.500017 assigned positive charge : 357.8471 centred at (gu) : 89.12758 89.55500 93.55684 assigned negative charge : -356.3476 centred at (gu) : 89.53853 90.51934 93.25484 start vw surface at 0.1600000 fill in re-entrant regions at 1.070000 boundary points on vw surface= 190971 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21066 grid for indexing accessible points = 1.400000 m= 100165 mr = 139255 m= 38171 mr = 82313 m= 9712 mr = 30839 m= 1751 mr = 7307 m= 191 mr = 1224 m= 9 mr = 131 m= 0 mr = 4 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.410000 number of dielectric boundary points 79897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.570000 number of grid points assigned charge 17736 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) : 2.085693 object centre at (A) : 22.84150 60.78350 1.469001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5040962 0.3125521 midg,1,midg; midg,igrid,midg 1.502887 -0.7418923 1,midg,midg; igrid,midg,midg -4.9948920E-02 -3.5639901E-02 gauss-seidel spectral radius is 0.9993023 estimated iterations to convergence 299 setup time was (sec) 2.740000 now iterating at: 13:40:12 rms-change max change #iterations 10.93791 457.0636 at 10iterations 6.510237 136.2571 at 20iterations 3.866341 73.39316 at 30iterations 2.294651 41.54196 at 40iterations 1.360524 25.00948 at 50iterations 0.8032901 14.41721 at 60iterations 0.4730790 9.144150 at 70iterations 0.2783002 4.783573 at 80iterations 0.1634837 2.913914 at 90iterations 9.6376471E-02 1.738216 at 100iterations 5.6642748E-02 0.9467468 at 110iterations 3.3511270E-02 0.5757027 at 120iterations 1.9871006E-02 0.3519859 at 130iterations 1.1945176E-02 0.2122421 at 140iterations 7.3424880E-03 0.1411943 at 150iterations 4.7039888E-03 9.9666595E-02 at 160iterations 3.1611740E-03 7.1338654E-02 at 170iterations 2.2629842E-03 4.8435211E-02 at 180iterations finished qdiffx linear iterations at : 13:40:26 total time elapsed so far: 16.59000 # loops : 180 mean,max change (kT/e) : 2.2629842E-03 4.8435211E-02 energy calculations done at 16.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.77000 DelPhi exited at 13:40:27 16.772u 0.299s 0:17.33 98.4% 0+0k 0+0io 0pf+0w