Sun Oct 9 14:15:30 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 14:15:30 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 = 2693 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: 0.5703391 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): 0.1880000 52.70400 ymin,ymax (A): -9.754000 39.84700 zmin,zma (A): -15.41100 47.00800 x,y,z range (A): 52.51600 49.60100 62.41900 scale (grids/A): 0.5703391 object centre (A): 26.44600 15.04650 15.79850 number of atom coordinates read : 2693 total number of charged atoms : 2553 net assigned charge : 7.000018 assigned positive charge : 407.5164 centred at (gu) : 89.53143 90.50076 88.45121 assigned negative charge : -400.5174 centred at (gu) : 89.48592 90.41703 88.49269 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5792 nv = 96 ne = 84 npr = 52706 no. pairs analyzed = 52706 no. exposed pairs = 3503 no. arc points = 24787 no. surface atoms = 1179 nbur = 1514 mkacc time = 0.1500000 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 = 1.512000 m= 267 mr = 2944 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3104 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2554 ## 312 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7404 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3953237E-09 3.4141781E-10 midg,1,midg; midg,igrid,midg -1.1597426E-10 2.5389508E-09 1,midg,midg; igrid,midg,midg 4.6080709E-10 1.5388990E-09 gauss-seidel spectral radius is 0.9841180 estimated iterations to convergence 65 setup time was (sec) 0.6300000 now iterating at: 14:15:30 rms-change max change #iterations 8.4518619E-02 14.24059 at 10iterations 6.2851114E-03 1.106518 at 20iterations 4.6731214E-04 8.0636978E-02 at 30iterations 3.7812348E-05 5.6610107E-03 at 40iterations 4.1849585E-06 8.1729889E-04 at 50iterations finished qdiffx linear iterations at : 14:15:34 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 4.1849585E-06 8.1729889E-04 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 14:15:34 4.120u 0.266s 0:04.71 92.9% 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 14:15:34 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 = 2693 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: 1.711017 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): 0.1880000 52.70400 ymin,ymax (A): -9.754000 39.84700 zmin,zma (A): -15.41100 47.00800 x,y,z range (A): 52.51600 49.60100 62.41900 scale (grids/A): 1.711017 object centre (A): 26.44600 15.04650 15.79850 number of atom coordinates read : 2693 total number of charged atoms : 2553 net assigned charge : 7.000018 assigned positive charge : 407.5164 centred at (gu) : 88.59361 91.50143 85.35300 assigned negative charge : -400.5174 centred at (gu) : 88.45753 91.25056 85.47773 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 63584 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24787 grid for indexing accessible points = 1.400000 m= 20152 mr = 42447 m= 2319 mr = 13610 m= 70 mr = 1116 m= 3 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 28948 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 260 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 19729 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) : 0.5703391 object centre at (A) : 26.44600 15.04650 15.79850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5276429E-02 1.0396508E-02 midg,1,midg; midg,igrid,midg 1.0686300E-03 4.0038200E-03 1,midg,midg; igrid,midg,midg -1.2015538E-02 -1.8826628E-03 gauss-seidel spectral radius is 0.9983307 estimated iterations to convergence 194 setup time was (sec) 0.8700000 now iterating at: 14:15:36 rms-change max change #iterations 3.454160 170.9721 at 10iterations 1.484018 76.52386 at 20iterations 0.6436694 24.47465 at 30iterations 0.2780000 10.05327 at 40iterations 0.1199009 5.061844 at 50iterations 5.1756185E-02 1.980309 at 60iterations 2.2389673E-02 0.8755684 at 70iterations 9.6528642E-03 0.3620536 at 80iterations 4.1889097E-03 0.1505351 at 90iterations 1.8115818E-03 6.1857224E-02 at 100iterations 7.8316708E-04 3.0620575E-02 at 110iterations 3.3888861E-04 1.2832642E-02 at 120iterations finished qdiffx linear iterations at : 14:15:44 total time elapsed so far: 9.080000 # loops : 120 mean,max change (kT/e) : 3.3888861E-04 1.2832642E-02 energy calculations done at 9.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.270000 DelPhi exited at 14:15:44 9.268u 0.292s 0:09.91 96.3% 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 14:15:44 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 = 2693 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: 2.566526 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): 0.1880000 52.70400 ymin,ymax (A): -9.754000 39.84700 zmin,zma (A): -15.41100 47.00800 x,y,z range (A): 52.51600 49.60100 62.41900 scale (grids/A): 2.566526 object centre (A): 26.44600 15.04650 15.79850 number of atom coordinates read : 2693 total number of charged atoms : 2553 net assigned charge : 7.000018 assigned positive charge : 407.5164 centred at (gu) : 87.89031 92.25198 83.02931 assigned negative charge : -400.5174 centred at (gu) : 87.68619 91.87589 83.21648 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 147693 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24787 grid for indexing accessible points = 1.400000 m= 68630 mr = 104244 m= 20466 mr = 53579 m= 3585 mr = 15236 m= 319 mr = 2286 m= 8 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.390000 number of dielectric boundary points 65211 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 20405 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) : 1.711017 object centre at (A) : 26.44600 15.04650 15.79850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9796238 0.1296382 midg,1,midg; midg,igrid,midg 2.2460167E-04 5.5987136E-03 1,midg,midg; igrid,midg,midg -0.1355607 -8.1530072E-02 gauss-seidel spectral radius is 0.9991786 estimated iterations to convergence 276 setup time was (sec) 1.720000 now iterating at: 14:15:46 rms-change max change #iterations 8.809885 311.3350 at 10iterations 5.069881 168.2323 at 20iterations 2.912464 71.26987 at 30iterations 1.655059 39.64851 at 40iterations 0.9366093 20.62458 at 50iterations 0.5287398 12.61964 at 60iterations 0.2981178 6.297662 at 70iterations 0.1669938 3.961624 at 80iterations 9.3879655E-02 1.811893 at 90iterations 5.2521054E-02 1.168842 at 100iterations 2.9416732E-02 0.7466736 at 110iterations 1.6449463E-02 0.3329115 at 120iterations 9.2100324E-03 0.1840129 at 130iterations 5.1353802E-03 0.1076756 at 140iterations 2.8720852E-03 5.9371948E-02 at 150iterations 1.6010581E-03 3.2031059E-02 at 160iterations 8.9441129E-04 1.8815041E-02 at 170iterations 4.9989804E-04 1.0781288E-02 at 180iterations finished qdiffx linear iterations at : 14:16:00 total time elapsed so far: 15.09000 # loops : 180 mean,max change (kT/e) : 4.9989804E-04 1.0781288E-02 energy calculations done at 15.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.26000 DelPhi exited at 14:16:00 15.267u 0.306s 0:15.83 98.2% 0+0k 0+0io 0pf+0w