Sat Oct 15 15:27:46 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 Sat Oct 15 2011 at 15:27:46 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 = 3339 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5278218 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): 112.4780 170.0320 ymin,ymax (A): 18.07600 65.76400 zmin,zma (A): -10.50800 56.93900 x,y,z range (A): 57.55400 47.68800 67.44701 scale (grids/A): 0.5278218 object centre (A): 141.2550 41.92000 23.21550 number of atom coordinates read : 3339 total number of charged atoms : 3186 net assigned charge : 0.5000231 assigned positive charge : 514.4705 centred at (gu) : 90.21218 90.07003 87.91622 assigned negative charge : -513.9716 centred at (gu) : 90.32965 90.18237 87.82922 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5776 nv = 96 ne = 84 npr = 67632 no. pairs analyzed = 67632 no. exposed pairs = 3957 no. arc points = 27791 no. surface atoms = 1336 nbur = 2003 mkacc time = 0.1200000 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 = 1.624000 m= 219 mr = 3024 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2848 ## 435 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7795 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3413762E-10 2.0546428E-10 midg,1,midg; midg,igrid,midg 4.3557713E-10 -4.1413595E-10 1,midg,midg; igrid,midg,midg 4.3767051E-10 -4.5089166E-10 gauss-seidel spectral radius is 0.9815280 estimated iterations to convergence 61 setup time was (sec) 0.4300000 now iterating at: 15:27:46 rms-change max change #iterations 6.7156427E-02 11.42180 at 10iterations 4.1804397E-03 0.8359947 at 20iterations 2.5611237E-04 4.1082382E-02 at 30iterations 1.7335558E-05 2.8305054E-03 at 40iterations 1.7014572E-06 3.9482117E-04 at 50iterations finished qdiffx linear iterations at : 15:27:50 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 1.7014572E-06 3.9482117E-04 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 15:27:50 3.570u 0.177s 0:04.28 87.3% 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 Sat Oct 15 2011 at 15:27:50 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 = 3339 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.583465 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): 112.4780 170.0320 ymin,ymax (A): 18.07600 65.76400 zmin,zma (A): -10.50800 56.93900 x,y,z range (A): 57.55400 47.68800 67.44701 scale (grids/A): 1.583465 object centre (A): 141.2550 41.92000 23.21550 number of atom coordinates read : 3339 total number of charged atoms : 3186 net assigned charge : 0.5000231 assigned positive charge : 514.4705 centred at (gu) : 90.63551 90.20909 83.74783 assigned negative charge : -513.9716 centred at (gu) : 90.98850 90.54672 83.48714 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 64082 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27791 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20036 mr = 43674 m= 1865 mr = 13932 m= 45 mr = 853 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1306 time to turn everything in is 0.3300000 number of dielectric boundary points 27569 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 409 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 24168 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) : 0.5278218 object centre at (A) : 141.2550 41.92000 23.21550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1885970E-02 1.3083154E-02 midg,1,midg; midg,igrid,midg 1.9561492E-03 -4.0389276E-03 1,midg,midg; igrid,midg,midg 1.6941775E-02 1.0514074E-03 gauss-seidel spectral radius is 0.9980889 estimated iterations to convergence 182 setup time was (sec) 0.5600000 now iterating at: 15:27:51 rms-change max change #iterations 3.354524 162.2021 at 10iterations 1.369486 51.91400 at 20iterations 0.5572665 20.54564 at 30iterations 0.2275825 8.335480 at 40iterations 9.2670888E-02 3.934000 at 50iterations 3.7893470E-02 1.295155 at 60iterations 1.5454264E-02 0.5820735 at 70iterations 6.2961639E-03 0.2403870 at 80iterations 2.5863789E-03 0.1093750 at 90iterations 1.0597605E-03 3.8108826E-02 at 100iterations 4.3296901E-04 1.4686584E-02 at 110iterations 1.7949661E-04 6.7052841E-03 at 120iterations finished qdiffx linear iterations at : 15:28:06 total time elapsed so far: 8.060000 # loops : 120 mean,max change (kT/e) : 1.7949661E-04 6.7052841E-03 energy calculations done at 8.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.190000 DelPhi exited at 15:28:06 8.196u 0.239s 0:16.30 51.6% 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 15:28:07 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 = 3339 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: 2.375198 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): 112.4780 170.0320 ymin,ymax (A): 18.07600 65.76400 zmin,zma (A): -10.50800 56.93900 x,y,z range (A): 57.55400 47.68800 67.44701 scale (grids/A): 2.375198 object centre (A): 141.2550 41.92000 23.21550 number of atom coordinates read : 3339 total number of charged atoms : 3186 net assigned charge : 0.5000231 assigned positive charge : 514.4705 centred at (gu) : 90.95293 90.31343 80.62159 assigned negative charge : -513.9716 centred at (gu) : 91.48269 90.81992 80.23061 start vw surface at 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 148785 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27791 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 69363 mr = 106554 m= 19759 mr = 55458 m= 2840 mr = 14750 m= 142 mr = 1732 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 4431 time to turn everything in is 0.8000000 number of dielectric boundary points 62351 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 38 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 25444 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) : 1.583465 object centre at (A) : 141.2550 41.92000 23.21550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1501499E-02 0.2726738 midg,1,midg; midg,igrid,midg 2.6497208E-02 -2.4343573E-02 1,midg,midg; igrid,midg,midg 0.2480156 3.2488950E-02 gauss-seidel spectral radius is 0.9991085 estimated iterations to convergence 265 setup time was (sec) 1.050000 now iterating at: 15:28:08 rms-change max change #iterations 8.736243 304.0977 at 10iterations 4.825773 122.9197 at 20iterations 2.647571 64.30186 at 30iterations 1.448405 38.15856 at 40iterations 0.7919235 20.36851 at 50iterations 0.4329504 9.809971 at 60iterations 0.2356010 5.428717 at 70iterations 0.1282683 2.812309 at 80iterations 6.9703005E-02 1.449883 at 90iterations 3.7955206E-02 0.8272686 at 100iterations 2.0616246E-02 0.4249690 at 110iterations 1.1208401E-02 0.2262933 at 120iterations 6.0834661E-03 0.1267471 at 130iterations 3.3147016E-03 7.2496414E-02 at 140iterations 1.8005712E-03 3.8432598E-02 at 150iterations 9.7865751E-04 1.8904924E-02 at 160iterations 5.3073984E-04 1.1393547E-02 at 170iterations 2.8904472E-04 6.0539246E-03 at 180iterations finished qdiffx linear iterations at : 15:28:23 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 2.8904472E-04 6.0539246E-03 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.29000 DelPhi exited at 15:28:24 13.290u 0.228s 0:17.23 78.4% 0+0k 0+0io 0pf+0w