Tue Oct 11 08:29:54 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 Tue Oct 11 2011 at 08:29:54 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3033 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6182165 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): -13.36700 44.21800 ymin,ymax (A): -9.081000 43.95500 zmin,zma (A): -25.52000 29.98600 x,y,z range (A): 57.58500 53.03600 55.50600 scale (grids/A): 0.6182165 object centre (A): 15.42550 17.43700 2.233000 number of atom coordinates read : 3033 total number of charged atoms : 2875 net assigned charge : -2.859981 assigned positive charge : 461.5830 centred at (gu) : 91.40189 90.29404 90.49541 assigned negative charge : -464.4439 centred at (gu) : 91.22416 90.12910 90.53276 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7276 nv = 96 ne = 84 npr = 63244 no. pairs analyzed = 63244 no. exposed pairs = 3589 no. arc points = 24403 no. surface atoms = 1206 nbur = 1827 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 306 mr = 4080 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3476 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2438 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9291 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6297892E-10 -5.8191230E-09 midg,1,midg; midg,igrid,midg -1.4103477E-08 1.0505643E-08 1,midg,midg; igrid,midg,midg -1.1768938E-08 1.4828532E-08 gauss-seidel spectral radius is 0.9864764 estimated iterations to convergence 70 setup time was (sec) 0.5300000 now iterating at: 08:29:55 rms-change max change #iterations 0.1344341 19.38046 at 10iterations 1.2457360E-02 1.860627 at 20iterations 1.2237508E-03 0.1687851 at 30iterations 1.4006464E-04 1.9042969E-02 at 40iterations 2.5884059E-05 3.2062531E-03 at 50iterations finished qdiffx linear iterations at : 08:29:57 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 2.5884059E-05 3.2062531E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 08:29:58 3.127u 0.141s 0:03.56 91.5% 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 Tue Oct 11 2011 at 08:29:58 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3033 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.854650 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): -13.36700 44.21800 ymin,ymax (A): -9.081000 43.95500 zmin,zma (A): -25.52000 29.98600 x,y,z range (A): 57.58500 53.03600 55.50600 scale (grids/A): 1.854650 object centre (A): 15.42550 17.43700 2.233000 number of atom coordinates read : 3033 total number of charged atoms : 2875 net assigned charge : -2.859981 assigned positive charge : 461.5830 centred at (gu) : 94.20509 90.88142 91.48531 assigned negative charge : -464.4439 centred at (gu) : 93.67197 90.38685 91.59810 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 80069 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24403 grid for indexing accessible points = 1.400000 m= 26757 mr = 56642 m= 3483 mr = 19404 m= 184 mr = 2063 m= 4 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1539 time to turn everything in is 0.5600000 number of dielectric boundary points 32350 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 204 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 22503 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) : 0.6182165 object centre at (A) : 15.42550 17.43700 2.233000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3313634E-02 -1.1898337E-02 midg,1,midg; midg,igrid,midg -3.2470882E-02 8.6114500E-03 1,midg,midg; igrid,midg,midg -6.9103958E-03 4.1368023E-02 gauss-seidel spectral radius is 0.9985933 estimated iterations to convergence 211 setup time was (sec) 0.8200000 now iterating at: 08:29:59 rms-change max change #iterations 4.438416 207.3606 at 10iterations 2.055785 67.66760 at 20iterations 0.9551605 32.38089 at 30iterations 0.4430965 14.00226 at 40iterations 0.2054726 6.444923 at 50iterations 9.5377281E-02 2.982648 at 60iterations 4.4250779E-02 1.440168 at 70iterations 2.0530293E-02 0.5951476 at 80iterations 9.5391329E-03 0.2958269 at 90iterations 4.4389437E-03 0.1303635 at 100iterations 2.0649920E-03 6.5812826E-02 at 110iterations 9.6412067E-04 2.9096603E-02 at 120iterations finished qdiffx linear iterations at : 08:30:05 total time elapsed so far: 6.980000 # loops : 120 mean,max change (kT/e) : 9.6412067E-04 2.9096603E-02 energy calculations done at 6.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.160000 DelPhi exited at 08:30:05 7.158u 0.159s 0:07.60 96.0% 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 Tue Oct 11 2011 at 08:30:05 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3033 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.781974 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): -13.36700 44.21800 ymin,ymax (A): -9.081000 43.95500 zmin,zma (A): -25.52000 29.98600 x,y,z range (A): 57.58500 53.03600 55.50600 scale (grids/A): 2.781974 object centre (A): 15.42550 17.43700 2.233000 number of atom coordinates read : 3033 total number of charged atoms : 2875 net assigned charge : -2.859981 assigned positive charge : 461.5830 centred at (gu) : 96.30733 91.32209 92.22785 assigned negative charge : -464.4439 centred at (gu) : 95.50787 90.58032 92.39701 start vw surface at 0.1700000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 185748 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24403 grid for indexing accessible points = 1.400000 m= 89878 mr = 137620 m= 28894 mr = 73091 m= 6044 mr = 22842 m= 794 mr = 4359 m= 47 mr = 476 m= 3 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 5151 time to turn everything in is 1.380000 number of dielectric boundary points 73008 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 22996 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) : 1.854650 object centre at (A) : 15.42550 17.43700 2.233000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4650906 2.5149154E-02 midg,1,midg; midg,igrid,midg -0.4199373 8.4714010E-02 1,midg,midg; igrid,midg,midg -3.6332645E-02 0.5667815 gauss-seidel spectral radius is 0.9992499 estimated iterations to convergence 288 setup time was (sec) 1.660000 now iterating at: 08:30:07 rms-change max change #iterations 10.40370 330.7633 at 10iterations 6.060962 154.1700 at 20iterations 3.503996 65.84949 at 30iterations 2.022644 42.59544 at 40iterations 1.168175 22.97520 at 50iterations 0.6716701 12.20433 at 60iterations 0.3856108 6.845943 at 70iterations 0.2217309 4.220407 at 80iterations 0.1273344 2.328563 at 90iterations 7.3039912E-02 1.277792 at 100iterations 4.1847263E-02 0.7416306 at 110iterations 2.4106419E-02 0.4273052 at 120iterations 1.3840570E-02 0.2474365 at 130iterations 7.9632616E-03 0.1496544 at 140iterations 4.5977822E-03 7.6442719E-02 at 150iterations 2.6642412E-03 4.7052145E-02 at 160iterations 1.5570174E-03 2.7732849E-02 at 170iterations 9.1948378E-04 1.6763687E-02 at 180iterations finished qdiffx linear iterations at : 08:30:17 total time elapsed so far: 10.96000 # loops : 180 mean,max change (kT/e) : 9.1948378E-04 1.6763687E-02 energy calculations done at 10.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.13000 DelPhi exited at 08:30:17 11.135u 0.174s 0:11.60 97.4% 0+0k 0+0io 0pf+0w