Mon Oct 10 17:02:19 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 Mon Oct 10 2011 at 17:02:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2893 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5814144 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): -30.74500 30.48500 ymin,ymax (A): -25.40500 21.79300 zmin,zma (A): -7.585000 41.66300 x,y,z range (A): 61.23000 47.19800 49.24800 scale (grids/A): 0.5814144 object centre (A): -0.1300001 -1.805999 17.03900 number of atom coordinates read : 2893 total number of charged atoms : 2753 net assigned charge : -0.4999793 assigned positive charge : 433.4590 centred at (gu) : 89.12998 89.52969 89.04921 assigned negative charge : -433.9602 centred at (gu) : 89.09957 89.65358 88.97284 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6300 nv = 96 ne = 84 npr = 58917 no. pairs analyzed = 58917 no. exposed pairs = 3768 no. arc points = 26397 no. surface atoms = 1260 nbur = 1633 mkacc time = 0.1300000 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 = 1.484000 m= 256 mr = 3178 m= 0 mr = 12 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.3100000 number of dielectric boundary points 3366 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2704 ## 272 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8149 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3018960E-09 1.2767541E-09 midg,1,midg; midg,igrid,midg 2.9574001E-09 -2.6197897E-09 1,midg,midg; igrid,midg,midg -9.6880515E-10 4.7076437E-10 gauss-seidel spectral radius is 0.9847239 estimated iterations to convergence 66 setup time was (sec) 0.5200000 now iterating at: 17:02:20 rms-change max change #iterations 9.5605053E-02 14.29287 at 10iterations 7.5100628E-03 1.116757 at 20iterations 5.7938450E-04 8.8209152E-02 at 30iterations 4.7561487E-05 7.3127747E-03 at 40iterations 3.6827091E-06 5.4740906E-04 at 50iterations finished qdiffx linear iterations at : 17:02:23 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 3.6827091E-06 5.4740906E-04 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 17:02:23 3.115u 0.134s 0:03.70 87.5% 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 Mon Oct 10 2011 at 17:02:23 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 = 2893 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.744243 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): -30.74500 30.48500 ymin,ymax (A): -25.40500 21.79300 zmin,zma (A): -7.585000 41.66300 x,y,z range (A): 61.23000 47.19800 49.24800 scale (grids/A): 1.744243 object centre (A): -0.1300001 -1.805999 17.03900 number of atom coordinates read : 2893 total number of charged atoms : 2753 net assigned charge : -0.4999793 assigned positive charge : 433.4590 centred at (gu) : 87.38875 88.58815 87.14674 assigned negative charge : -433.9602 centred at (gu) : 87.29842 88.96040 86.91838 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 68868 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26397 grid for indexing accessible points = 1.400000 m= 21470 mr = 45810 m= 2468 mr = 14589 m= 80 mr = 1203 m= 0 mr = 10 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 940 time to turn everything in is 0.4700000 number of dielectric boundary points 31274 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 207 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 21400 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) : 0.5814144 object centre at (A) : -0.1300001 -1.805999 17.03900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4360285E-03 3.9492224E-05 midg,1,midg; midg,igrid,midg 1.6724190E-02 -1.7484132E-02 1,midg,midg; igrid,midg,midg -4.6903272E-03 9.6649714E-03 gauss-seidel spectral radius is 0.9984041 estimated iterations to convergence 199 setup time was (sec) 0.7300000 now iterating at: 17:02:24 rms-change max change #iterations 3.734824 164.7852 at 10iterations 1.635565 71.55756 at 20iterations 0.7173991 27.05318 at 30iterations 0.3159035 10.55877 at 40iterations 0.1387928 4.753048 at 50iterations 6.0886543E-02 1.900357 at 60iterations 2.6863437E-02 0.9014659 at 70iterations 1.1818253E-02 0.4658136 at 80iterations 5.2028135E-03 0.1771851 at 90iterations 2.2842700E-03 7.9942703E-02 at 100iterations 1.0053610E-03 3.4515381E-02 at 110iterations 4.4364206E-04 1.4694214E-02 at 120iterations finished qdiffx linear iterations at : 17:02:30 total time elapsed so far: 6.710000 # loops : 120 mean,max change (kT/e) : 4.4364206E-04 1.4694214E-02 energy calculations done at 6.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.880000 DelPhi exited at 17:02:31 6.887u 0.199s 0:07.69 91.9% 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 Mon Oct 10 2011 at 17:02:31 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 = 2893 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: 2.616365 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): -30.74500 30.48500 ymin,ymax (A): -25.40500 21.79300 zmin,zma (A): -7.585000 41.66300 x,y,z range (A): 61.23000 47.19800 49.24800 scale (grids/A): 2.616365 object centre (A): -0.1300001 -1.805999 17.03900 number of atom coordinates read : 2893 total number of charged atoms : 2753 net assigned charge : -0.4999793 assigned positive charge : 433.4590 centred at (gu) : 86.08308 87.88200 85.71986 assigned negative charge : -433.9602 centred at (gu) : 85.94753 88.44037 85.37753 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 159680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26397 grid for indexing accessible points = 1.400000 m= 72817 mr = 112032 m= 21782 mr = 56853 m= 3900 mr = 16264 m= 328 mr = 2507 m= 4 mr = 161 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 3233 time to turn everything in is 1.160000 number of dielectric boundary points 70694 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 22009 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) : 1.744243 object centre at (A) : -0.1300001 -1.805999 17.03900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3289334E-02 -2.7146179E-02 midg,1,midg; midg,igrid,midg 0.2305268 -0.1872411 1,midg,midg; igrid,midg,midg -2.1963641E-02 0.3815143 gauss-seidel spectral radius is 0.9992059 estimated iterations to convergence 280 setup time was (sec) 1.430000 now iterating at: 17:02:33 rms-change max change #iterations 9.377585 270.7780 at 10iterations 5.387616 133.8713 at 20iterations 3.078837 71.14013 at 30iterations 1.745541 39.10332 at 40iterations 0.9871083 20.99794 at 50iterations 0.5589023 12.46831 at 60iterations 0.3152618 6.736794 at 70iterations 0.1779044 3.839475 at 80iterations 0.1002379 2.057671 at 90iterations 5.6503903E-02 1.152557 at 100iterations 3.1786155E-02 0.5823326 at 110iterations 1.7860144E-02 0.3321838 at 120iterations 1.0053347E-02 0.2003822 at 130iterations 5.6621432E-03 0.1111221 at 140iterations 3.1815218E-03 6.2672615E-02 at 150iterations 1.7944113E-03 3.6740124E-02 at 160iterations 1.0092421E-03 1.8054962E-02 at 170iterations 5.6808291E-04 1.0782242E-02 at 180iterations finished qdiffx linear iterations at : 17:02:43 total time elapsed so far: 12.06000 # loops : 180 mean,max change (kT/e) : 5.6808291E-04 1.0782242E-02 energy calculations done at 12.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.23000 DelPhi exited at 17:02:45 12.235u 0.193s 0:13.75 90.3% 0+0k 0+0io 0pf+0w