Sun Oct 9 01:52:56 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 01:52:56 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 = 2395 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: 0.6366124 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): 10.98900 66.78400 ymin,ymax (A): -30.40900 25.51200 zmin,zma (A): 3.032000 45.50400 x,y,z range (A): 55.79500 55.92100 42.47200 scale (grids/A): 0.6366124 object centre (A): 38.88650 -2.448500 24.26800 number of atom coordinates read : 2395 total number of charged atoms : 2259 net assigned charge : 9.500027 assigned positive charge : 350.0043 centred at (gu) : 90.72489 90.90495 88.86775 assigned negative charge : -340.5050 centred at (gu) : 90.68272 90.91581 89.01614 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6821 nv = 96 ne = 84 npr = 47021 no. pairs analyzed = 47021 no. exposed pairs = 3223 no. arc points = 23212 no. surface atoms = 1065 nbur = 1330 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 382 mr = 3514 m= 3 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 76 time to turn everything in is 0.2600000 number of dielectric boundary points 3648 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2231 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7960 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3059607E-08 -1.2084730E-09 midg,1,midg; midg,igrid,midg 1.1055270E-08 1.3646581E-08 1,midg,midg; igrid,midg,midg 7.2448159E-09 1.8916694E-08 gauss-seidel spectral radius is 0.9872117 estimated iterations to convergence 72 setup time was (sec) 0.4700000 now iterating at: 01:52:57 rms-change max change #iterations 0.1310460 23.52433 at 10iterations 1.2851442E-02 1.751825 at 20iterations 1.2535439E-03 0.2107668 at 30iterations 1.2782605E-04 1.8032074E-02 at 40iterations 1.4215685E-05 2.0465851E-03 at 50iterations finished qdiffx linear iterations at : 01:52:59 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 1.4215685E-05 2.0465851E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 01:53:00 3.129u 0.150s 0:03.55 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 Sun Oct 9 2011 at 01:53:00 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 = 2395 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: 1.909837 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): 10.98900 66.78400 ymin,ymax (A): -30.40900 25.51200 zmin,zma (A): 3.032000 45.50400 x,y,z range (A): 55.79500 55.92100 42.47200 scale (grids/A): 1.909837 object centre (A): 38.88650 -2.448500 24.26800 number of atom coordinates read : 2395 total number of charged atoms : 2259 net assigned charge : 9.500027 assigned positive charge : 350.0043 centred at (gu) : 92.17426 92.71423 86.60290 assigned negative charge : -340.5050 centred at (gu) : 92.04805 92.74734 87.04840 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 72908 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23212 grid for indexing accessible points = 1.400000 m= 25689 mr = 48699 m= 4246 mr = 18175 m= 265 mr = 2557 m= 2 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 2659 time to turn everything in is 0.5200000 number of dielectric boundary points 33585 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 17805 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) : 0.6366124 object centre at (A) : 38.88650 -2.448500 24.26800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4280229E-02 -7.4039618E-03 midg,1,midg; midg,igrid,midg 5.1866699E-02 3.1355415E-02 1,midg,midg; igrid,midg,midg 1.1861923E-02 4.8644960E-02 gauss-seidel spectral radius is 0.9986360 estimated iterations to convergence 215 setup time was (sec) 0.7800000 now iterating at: 01:53:01 rms-change max change #iterations 3.936315 167.9618 at 10iterations 1.842501 72.19896 at 20iterations 0.8630522 34.21363 at 30iterations 0.4013600 16.04964 at 40iterations 0.1876751 6.030450 at 50iterations 8.7717615E-02 2.712749 at 60iterations 4.1129161E-02 1.406765 at 70iterations 1.9197704E-02 0.5843048 at 80iterations 9.0201180E-03 0.2875452 at 90iterations 4.2126020E-03 0.1404686 at 100iterations 1.9736423E-03 6.2756896E-02 at 110iterations 9.2486572E-04 3.0614853E-02 at 120iterations finished qdiffx linear iterations at : 01:53:07 total time elapsed so far: 6.780000 # loops : 120 mean,max change (kT/e) : 9.2486572E-04 3.0614853E-02 energy calculations done at 6.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.950000 DelPhi exited at 01:53:07 6.955u 0.160s 0:07.39 96.2% 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 01:53:07 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 = 2395 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: 2.864756 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): 10.98900 66.78400 ymin,ymax (A): -30.40900 25.51200 zmin,zma (A): 3.032000 45.50400 x,y,z range (A): 55.79500 55.92100 42.47200 scale (grids/A): 2.864756 object centre (A): 38.88650 -2.448500 24.26800 number of atom coordinates read : 2395 total number of charged atoms : 2259 net assigned charge : 9.500027 assigned positive charge : 350.0043 centred at (gu) : 93.26129 94.07124 84.90427 assigned negative charge : -340.5050 centred at (gu) : 93.07210 94.12101 85.57262 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 168348 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23212 grid for indexing accessible points = 1.400000 m= 82906 mr = 118762 m= 30205 mr = 66002 m= 7675 mr = 23559 m= 1246 mr = 5682 m= 100 mr = 822 m= 3 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 9341 time to turn everything in is 1.260000 number of dielectric boundary points 75611 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 18071 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) : 1.909837 object centre at (A) : 38.88650 -2.448500 24.26800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3420332 -7.9780228E-02 midg,1,midg; midg,igrid,midg 0.7449830 0.3217186 1,midg,midg; igrid,midg,midg 0.2187437 0.4800587 gauss-seidel spectral radius is 0.9992716 estimated iterations to convergence 292 setup time was (sec) 1.540000 now iterating at: 01:53:09 rms-change max change #iterations 9.508782 315.5982 at 10iterations 5.620266 149.8397 at 20iterations 3.288096 67.45333 at 30iterations 1.930884 50.00226 at 40iterations 1.121796 22.56570 at 50iterations 0.6513723 12.57064 at 60iterations 0.3784361 7.772381 at 70iterations 0.2197131 4.135844 at 80iterations 0.1269675 2.775914 at 90iterations 7.3650353E-02 1.389767 at 100iterations 4.2573571E-02 0.8502197 at 110iterations 2.4552174E-02 0.5083094 at 120iterations 1.4203760E-02 0.2563396 at 130iterations 8.1901196E-03 0.1434250 at 140iterations 4.7406456E-03 0.1000502 at 150iterations 2.7320508E-03 5.2057743E-02 at 160iterations 1.5793195E-03 2.9117584E-02 at 170iterations 9.1193180E-04 1.6593933E-02 at 180iterations finished qdiffx linear iterations at : 01:53:18 total time elapsed so far: 11.01000 # loops : 180 mean,max change (kT/e) : 9.1193180E-04 1.6593933E-02 energy calculations done at 11.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.19000 DelPhi exited at 01:53:19 11.190u 0.176s 0:11.63 97.6% 0+0k 0+0io 0pf+0w