Sun Oct 9 13:22:07 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 Sun Oct 9 2011 at 13:22:08 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2367 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6699538 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): -7.141000 44.64600 ymin,ymax (A): 22.17600 75.31400 zmin,zma (A): 41.59200 84.03200 x,y,z range (A): 51.78700 53.13799 42.44000 scale (grids/A): 0.6699538 object centre (A): 18.75250 48.74500 62.81200 number of atom coordinates read : 2367 total number of charged atoms : 2226 net assigned charge : 4.500020 assigned positive charge : 364.7962 centred at (gu) : 89.75841 90.38668 90.52533 assigned negative charge : -360.2966 centred at (gu) : 89.72173 90.55959 90.63622 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7215 nv = 96 ne = 84 npr = 47005 no. pairs analyzed = 47005 no. exposed pairs = 2961 no. arc points = 21187 no. surface atoms = 995 nbur = 1372 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 423 mr = 3941 m= 5 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3632 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2141 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8360 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7007020E-08 -1.2569916E-08 midg,1,midg; midg,igrid,midg 5.1179104E-08 -2.8542601E-08 1,midg,midg; igrid,midg,midg 6.9358874E-09 2.2812054E-08 gauss-seidel spectral radius is 0.9884301 estimated iterations to convergence 76 setup time was (sec) 0.5400000 now iterating at: 13:22:08 rms-change max change #iterations 0.1690408 25.42932 at 10iterations 1.9090127E-02 2.678108 at 20iterations 2.5042421E-03 0.4353180 at 30iterations 5.5656006E-04 9.3986511E-02 at 40iterations 1.7351107E-04 3.2014847E-02 at 50iterations finished qdiffx linear iterations at : 13:22:11 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.7351107E-04 3.2014847E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 13:22:11 3.406u 0.149s 0:03.84 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 13:22:11 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2367 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: 2.009861 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): -7.141000 44.64600 ymin,ymax (A): 22.17600 75.31400 zmin,zma (A): 41.59200 84.03200 x,y,z range (A): 51.78700 53.13799 42.44000 scale (grids/A): 2.009861 object centre (A): 18.75250 48.74500 62.81200 number of atom coordinates read : 2367 total number of charged atoms : 2226 net assigned charge : 4.500020 assigned positive charge : 364.7962 centred at (gu) : 89.27474 91.15984 91.57561 assigned negative charge : -360.2966 centred at (gu) : 89.16501 91.67860 91.90833 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 76680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21187 grid for indexing accessible points = 1.400000 m= 29114 mr = 52910 m= 5113 mr = 21649 m= 421 mr = 3267 m= 9 mr = 188 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 33323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 17624 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) : 0.6699538 object centre at (A) : 18.75250 48.74500 62.81200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0011098E-02 -1.7141110E-03 midg,1,midg; midg,igrid,midg 1.4760000E-02 -4.3506004E-02 1,midg,midg; igrid,midg,midg 4.9027093E-02 1.4631907E-02 gauss-seidel spectral radius is 0.9987510 estimated iterations to convergence 224 setup time was (sec) 0.8600000 now iterating at: 13:22:12 rms-change max change #iterations 4.535347 281.7094 at 10iterations 2.179446 83.69458 at 20iterations 1.060906 34.96278 at 30iterations 0.5103878 16.53148 at 40iterations 0.2471923 7.788452 at 50iterations 0.1201949 3.725822 at 60iterations 5.8321901E-02 1.699593 at 70iterations 2.8303446E-02 0.8724823 at 80iterations 1.3842224E-02 0.4546695 at 90iterations 6.8235006E-03 0.2110291 at 100iterations 3.4163741E-03 0.1115589 at 110iterations 1.7707254E-03 6.2537193E-02 at 120iterations finished qdiffx linear iterations at : 13:22:19 total time elapsed so far: 7.380000 # loops : 120 mean,max change (kT/e) : 1.7707254E-03 6.2537193E-02 energy calculations done at 7.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.570000 DelPhi exited at 13:22:19 7.570u 0.165s 0:08.01 96.5% 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 13:22:20 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2367 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: 3.014792 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): -7.141000 44.64600 ymin,ymax (A): 22.17600 75.31400 zmin,zma (A): 41.59200 84.03200 x,y,z range (A): 51.78700 53.13799 42.44000 scale (grids/A): 3.014792 object centre (A): 18.75250 48.74500 62.81200 number of atom coordinates read : 2367 total number of charged atoms : 2226 net assigned charge : 4.500020 assigned positive charge : 364.7962 centred at (gu) : 88.91208 91.73965 92.36339 assigned negative charge : -360.2966 centred at (gu) : 88.74754 92.51787 92.86249 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 176637 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21187 grid for indexing accessible points = 1.400000 m= 92200 mr = 127904 m= 35539 mr = 75426 m= 9588 mr = 28863 m= 1742 mr = 7236 m= 161 mr = 1236 m= 2 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.500000 number of dielectric boundary points 75130 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 17808 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) : 2.009861 object centre at (A) : 18.75250 48.74500 62.81200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4883771 -0.1153842 midg,1,midg; midg,igrid,midg 0.3160394 -0.5157168 1,midg,midg; igrid,midg,midg 0.6892064 -3.2443725E-02 gauss-seidel spectral radius is 0.9992803 estimated iterations to convergence 294 setup time was (sec) 1.800000 now iterating at: 13:22:21 rms-change max change #iterations 10.38214 397.0389 at 10iterations 6.112541 149.7456 at 20iterations 3.597261 76.09509 at 30iterations 2.105060 40.23879 at 40iterations 1.230454 22.83151 at 50iterations 0.7203177 14.04124 at 60iterations 0.4195952 8.078609 at 70iterations 0.2444288 4.677933 at 80iterations 0.1423581 2.591141 at 90iterations 8.2824968E-02 1.875793 at 100iterations 4.8285969E-02 0.8929424 at 110iterations 2.8264759E-02 0.5213795 at 120iterations 1.6573820E-02 0.3330784 at 130iterations 9.8729841E-03 0.1813478 at 140iterations 5.9986208E-03 0.1153698 at 150iterations 3.7798539E-03 7.6629639E-02 at 160iterations 2.5084054E-03 5.9879303E-02 at 170iterations 1.7738946E-03 4.0263176E-02 at 180iterations finished qdiffx linear iterations at : 13:22:32 total time elapsed so far: 12.15000 # loops : 180 mean,max change (kT/e) : 1.7738946E-03 4.0263176E-02 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.34000 DelPhi exited at 13:22:32 12.339u 0.190s 0:12.81 97.7% 0+0k 0+0io 0pf+0w