Sat Oct 8 13:01:59 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+sph2.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 = amb2.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 Sat Oct 8 2011 at 13:01:59 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3067 !!! WARNING: GLU 329 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.5768171 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): -23.68300 27.57900 ymin,ymax (A): -26.06800 24.78900 zmin,zma (A): -8.698999 53.01900 x,y,z range (A): 51.26200 50.85700 61.71800 scale (grids/A): 0.5768171 object centre (A): 1.948000 -0.6395006 22.16000 number of atom coordinates read : 3067 total number of charged atoms : 2919 net assigned charge : 5.226042 assigned positive charge : 459.6009 centred at (gu) : 91.03204 89.89500 90.10465 assigned negative charge : -454.3759 centred at (gu) : 91.14269 89.91000 90.23264 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6658 nv = 96 ne = 84 npr = 62368 no. pairs analyzed = 62368 no. exposed pairs = 3850 no. arc points = 27061 no. surface atoms = 1290 nbur = 1777 mkacc time = 0.1600000 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= 292 mr = 3565 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3374 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2771 ## 338 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8628 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5136272E-09 -1.6169192E-09 midg,1,midg; midg,igrid,midg 1.3887331E-09 7.3148704E-10 1,midg,midg; igrid,midg,midg 2.5602582E-09 -1.5747343E-09 gauss-seidel spectral radius is 0.9844944 estimated iterations to convergence 66 setup time was (sec) 0.6900000 now iterating at: 13:02:00 rms-change max change #iterations 9.9258453E-02 15.35801 at 10iterations 8.0118766E-03 1.267239 at 20iterations 1.2741543E-03 0.2627239 at 30iterations 5.1815069E-04 0.1150723 at 40iterations 2.3411073E-04 5.2148819E-02 at 50iterations finished qdiffx linear iterations at : 13:02:05 total time elapsed so far: 5.080000 # loops : 50 mean,max change (kT/e) : 2.3411073E-04 5.2148819E-02 energy calculations done at 5.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.250000 DelPhi exited at 13:02:05 5.257u 0.456s 0:05.97 95.4% 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 Sat Oct 8 2011 at 13:02:05 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3067 !!! WARNING: GLU 329 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.730451 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): -23.68300 27.57900 ymin,ymax (A): -26.06800 24.78900 zmin,zma (A): -8.698999 53.01900 x,y,z range (A): 51.26200 50.85700 61.71800 scale (grids/A): 1.730451 object centre (A): 1.948000 -0.6395006 22.16000 number of atom coordinates read : 3067 total number of charged atoms : 2919 net assigned charge : 5.226042 assigned positive charge : 459.6009 centred at (gu) : 93.09489 89.68431 90.31269 assigned negative charge : -454.3759 centred at (gu) : 93.42780 89.72977 90.69767 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73646 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27061 grid for indexing accessible points = 1.400000 m= 23744 mr = 50788 m= 2761 mr = 16683 m= 88 mr = 1429 m= 4 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 194 time to turn everything in is 0.6200000 number of dielectric boundary points 31336 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 268 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 22613 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) : 0.5768171 object centre at (A) : 1.948000 -0.6395006 22.16000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9556593E-02 1.9236011E-02 midg,1,midg; midg,igrid,midg 7.6547591E-03 5.0832839E-03 1,midg,midg; igrid,midg,midg 6.4016548E-03 -4.1247713E-03 gauss-seidel spectral radius is 0.9984020 estimated iterations to convergence 198 setup time was (sec) 0.9600000 now iterating at: 13:02:07 rms-change max change #iterations 3.844189 150.9724 at 10iterations 1.678505 55.72909 at 20iterations 0.7384142 28.45193 at 30iterations 0.3253658 11.23195 at 40iterations 0.1435985 6.207108 at 50iterations 6.3127354E-02 2.078644 at 60iterations 2.8048970E-02 0.9897041 at 70iterations 1.2510867E-02 0.4181671 at 80iterations 5.7611987E-03 0.2082138 at 90iterations 2.8841074E-03 0.1111965 at 100iterations 1.6148030E-03 6.4262390E-02 at 110iterations 1.0454796E-03 4.4830322E-02 at 120iterations finished qdiffx linear iterations at : 13:02:18 total time elapsed so far: 12.27000 # loops : 120 mean,max change (kT/e) : 1.0454796E-03 4.4830322E-02 energy calculations done at 12.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.43000 DelPhi exited at 13:02:19 12.433u 0.535s 0:13.24 97.8% 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 Sat Oct 8 2011 at 13:02:19 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3067 !!! WARNING: GLU 329 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.595677 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): -23.68300 27.57900 ymin,ymax (A): -26.06800 24.78900 zmin,zma (A): -8.698999 53.01900 x,y,z range (A): 51.26200 50.85700 61.71800 scale (grids/A): 2.595677 object centre (A): 1.948000 -0.6395006 22.16000 number of atom coordinates read : 3067 total number of charged atoms : 2919 net assigned charge : 5.226042 assigned positive charge : 459.6009 centred at (gu) : 94.64228 89.52637 90.46882 assigned negative charge : -454.3759 centred at (gu) : 95.14148 89.59455 91.04642 start vw surface at 0.1400000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 171152 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27061 grid for indexing accessible points = 1.400000 m= 80974 mr = 124064 m= 24276 mr = 64841 m= 4351 mr = 18544 m= 383 mr = 2868 m= 13 mr = 175 m= 0 mr = 2 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 705 time to turn everything in is 1.610000 number of dielectric boundary points 70655 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 23331 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) : 1.730451 object centre at (A) : 1.948000 -0.6395006 22.16000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2728099E-02 0.5521693 midg,1,midg; midg,igrid,midg 0.1081600 9.4873942E-02 1,midg,midg; igrid,midg,midg 4.0073484E-02 -5.1430695E-02 gauss-seidel spectral radius is 0.9992033 estimated iterations to convergence 280 setup time was (sec) 1.990000 now iterating at: 13:02:21 rms-change max change #iterations 9.489737 261.5035 at 10iterations 5.432419 121.9117 at 20iterations 3.105183 75.80087 at 30iterations 1.761688 48.81182 at 40iterations 0.9995196 20.95585 at 50iterations 0.5644447 12.50880 at 60iterations 0.3195964 7.009071 at 70iterations 0.1806355 3.482660 at 80iterations 0.1019563 2.096399 at 90iterations 5.7534933E-02 1.148099 at 100iterations 3.2511529E-02 0.8119850 at 110iterations 1.8446874E-02 0.4163551 at 120iterations 1.0495471E-02 0.2139950 at 130iterations 6.0834894E-03 0.1229706 at 140iterations 3.6418901E-03 8.8600159E-02 at 150iterations 2.2917369E-03 5.1645279E-02 at 160iterations 1.5625608E-03 4.2877197E-02 at 170iterations 1.1486462E-03 2.8917313E-02 at 180iterations finished qdiffx linear iterations at : 13:02:40 total time elapsed so far: 21.02000 # loops : 180 mean,max change (kT/e) : 1.1486462E-03 2.8917313E-02 energy calculations done at 21.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.18000 DelPhi exited at 13:02:41 21.183u 0.562s 0:22.00 98.8% 0+0k 0+0io 0pf+0w