Sat Oct 15 14:00:57 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 15 2011 at 14:00:59 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4304 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5126876 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): -15.92800 37.26700 ymin,ymax (A): -32.02800 31.30900 zmin,zma (A): -3.858000 65.58000 x,y,z range (A): 53.19500 63.33700 69.43800 scale (grids/A): 0.5126876 object centre (A): 10.66950 -0.3594999 30.86100 number of atom coordinates read : 4304 total number of charged atoms : 4098 net assigned charge : -1.193977 assigned positive charge : 643.7383 centred at (gu) : 90.12697 90.60134 87.67904 assigned negative charge : -644.9362 centred at (gu) : 89.98894 90.65456 87.80145 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7095 nv = 96 ne = 84 npr = 87976 no. pairs analyzed = 87976 no. exposed pairs = 5651 no. arc points = 38970 no. surface atoms = 1878 nbur = 2426 mkacc time = 0.2300000 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 = 1.652000 m= 272 mr = 3614 m= 0 mr = 9 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 3744 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3705 ## 547 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 9562 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2640037E-10 -1.8603925E-10 midg,1,midg; midg,igrid,midg 9.2538054E-11 -1.9013771E-10 1,midg,midg; igrid,midg,midg -3.7056486E-10 3.2999098E-10 gauss-seidel spectral radius is 0.9805085 estimated iterations to convergence 59 setup time was (sec) 0.7800000 now iterating at: 14:01:02 rms-change max change #iterations 6.5968931E-02 10.84043 at 10iterations 3.9092558E-03 0.5820971 at 20iterations 2.6790967E-04 4.2045593E-02 at 30iterations 4.7044821E-05 6.2065125E-03 at 40iterations 1.4747381E-05 1.9214153E-03 at 50iterations finished qdiffx linear iterations at : 14:01:12 total time elapsed so far: 5.310000 # loops : 50 mean,max change (kT/e) : 1.4747381E-05 1.9214153E-03 energy calculations done at 5.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.490000 DelPhi exited at 14:01:14 5.492u 0.462s 0:14.41 41.2% 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 Sat Oct 15 2011 at 14:01:15 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4304 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.538063 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): -15.92800 37.26700 ymin,ymax (A): -32.02800 31.30900 zmin,zma (A): -3.858000 65.58000 x,y,z range (A): 53.19500 63.33700 69.43800 scale (grids/A): 1.538063 object centre (A): 10.66950 -0.3594999 30.86100 number of atom coordinates read : 4304 total number of charged atoms : 4098 net assigned charge : -1.193977 assigned positive charge : 643.7383 centred at (gu) : 90.38003 91.80270 83.03584 assigned negative charge : -644.9362 centred at (gu) : 89.96621 91.96326 83.40401 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 80116 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38970 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 22686 mr = 54301 m= 2008 mr = 14659 m= 44 mr = 791 m= 0 mr = 2 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 134 time to turn everything in is 0.7100000 number of dielectric boundary points 35101 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 512 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 30889 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) : 0.5126876 object centre at (A) : 10.66950 -0.3594999 30.86100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1531486E-03 -1.4327448E-02 midg,1,midg; midg,igrid,midg -4.4610291E-03 -1.0108607E-02 1,midg,midg; igrid,midg,midg -4.2699771E-03 8.6249877E-03 gauss-seidel spectral radius is 0.9980819 estimated iterations to convergence 181 setup time was (sec) 1.050000 now iterating at: 14:01:17 rms-change max change #iterations 3.631690 179.3424 at 10iterations 1.466740 48.97772 at 20iterations 0.5979673 20.72341 at 30iterations 0.2429047 8.219069 at 40iterations 9.8638050E-02 3.256173 at 50iterations 4.0172119E-02 1.303719 at 60iterations 1.6403340E-02 0.5258765 at 70iterations 6.7085708E-03 0.2328911 at 80iterations 2.7471897E-03 9.9188328E-02 at 90iterations 1.1367127E-03 3.8440704E-02 at 100iterations 4.7907775E-04 1.6146183E-02 at 110iterations 2.1215467E-04 7.6951981E-03 at 120iterations finished qdiffx linear iterations at : 14:01:41 total time elapsed so far: 12.38000 # loops : 120 mean,max change (kT/e) : 2.1215467E-04 7.6951981E-03 energy calculations done at 12.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.56000 DelPhi exited at 14:01:42 12.565u 0.554s 0:27.38 47.8% 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 15 2011 at 14:01:43 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4304 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.307094 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): -15.92800 37.26700 ymin,ymax (A): -32.02800 31.30900 zmin,zma (A): -3.858000 65.58000 x,y,z range (A): 53.19500 63.33700 69.43800 scale (grids/A): 2.307094 object centre (A): 10.66950 -0.3594999 30.86100 number of atom coordinates read : 4304 total number of charged atoms : 4098 net assigned charge : -1.193977 assigned positive charge : 643.7383 centred at (gu) : 90.56950 92.70371 79.55344 assigned negative charge : -644.9362 centred at (gu) : 89.94917 92.94478 80.10596 start vw surface at 0.1700000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 186950 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38970 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 81776 mr = 133862 m= 20203 mr = 62976 m= 2784 mr = 14041 m= 135 mr = 1626 m= 0 mr = 24 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 422 time to turn everything in is 1.740000 number of dielectric boundary points 79319 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 32724 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) : 1.538063 object centre at (A) : 10.66950 -0.3594999 30.86100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1561415 -0.3000340 midg,1,midg; midg,igrid,midg -0.1164260 -0.2309250 1,midg,midg; igrid,midg,midg -5.6579392E-02 0.1173071 gauss-seidel spectral radius is 0.9991431 estimated iterations to convergence 270 setup time was (sec) 2.150000 now iterating at: 14:01:49 rms-change max change #iterations 9.842591 292.4854 at 10iterations 5.608812 135.2337 at 20iterations 3.171932 74.53825 at 30iterations 1.781110 43.91357 at 40iterations 0.9989658 23.36182 at 50iterations 0.5573854 12.10800 at 60iterations 0.3107443 6.941454 at 70iterations 0.1728576 3.296212 at 80iterations 9.5808193E-02 2.117432 at 90iterations 5.3050149E-02 1.143454 at 100iterations 2.9387942E-02 0.7166672 at 110iterations 1.6272066E-02 0.3383675 at 120iterations 8.9809904E-03 0.1856337 at 130iterations 4.9539399E-03 0.1040955 at 140iterations 2.7376963E-03 5.7104111E-02 at 150iterations 1.5150266E-03 2.8551102E-02 at 160iterations 8.3615631E-04 1.6418457E-02 at 170iterations 4.6197508E-04 9.1629028E-03 at 180iterations finished qdiffx linear iterations at : 14:02:18 total time elapsed so far: 21.31000 # loops : 180 mean,max change (kT/e) : 4.6197508E-04 9.1629028E-03 energy calculations done at 21.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.49000 DelPhi exited at 14:02:19 21.497u 0.540s 0:36.19 60.8% 0+0k 0+0io 0pf+0w