Mon Oct 10 14:10:03 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 14:10:03 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 = 4114 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5058542 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): 4.118000 74.49400 ymin,ymax (A): 42.90300 105.9030 zmin,zma (A): -12.22500 52.26700 x,y,z range (A): 70.37601 63.00000 64.49200 scale (grids/A): 0.5058542 object centre (A): 39.30600 74.40300 20.02100 number of atom coordinates read : 4114 total number of charged atoms : 3964 net assigned charge : -1.499993 assigned positive charge : 624.8716 centred at (gu) : 90.53235 90.76318 93.39146 assigned negative charge : -626.3754 centred at (gu) : 90.57948 90.67331 93.40285 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6954 nv = 96 ne = 84 npr = 77430 no. pairs analyzed = 77430 no. exposed pairs = 5822 no. arc points = 41508 no. surface atoms = 1925 nbur = 2189 mkacc time = 0.2200000 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 = 1.680000 m= 252 mr = 3251 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 3955 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4014 ## 627 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 9236 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2666787E-12 -9.4269863E-11 midg,1,midg; midg,igrid,midg -1.4890898E-10 1.7823791E-10 1,midg,midg; igrid,midg,midg 5.9170988E-11 -1.1924900E-10 gauss-seidel spectral radius is 0.9799853 estimated iterations to convergence 58 setup time was (sec) 0.7400000 now iterating at: 14:10:04 rms-change max change #iterations 5.8103181E-02 12.91975 at 10iterations 3.1993159E-03 0.5299690 at 20iterations 2.7561784E-04 4.5734406E-02 at 30iterations 5.2294719E-05 1.0629654E-02 at 40iterations 1.2449736E-05 2.8066635E-03 at 50iterations finished qdiffx linear iterations at : 14:10:07 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 1.2449736E-05 2.8066635E-03 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 14:10:08 4.237u 0.264s 0:04.86 92.3% 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 Mon Oct 10 2011 at 14:10:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4114 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.517563 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): 4.118000 74.49400 ymin,ymax (A): 42.90300 105.9030 zmin,zma (A): -12.22500 52.26700 x,y,z range (A): 70.37601 63.00000 64.49200 scale (grids/A): 1.517563 object centre (A): 39.30600 74.40300 20.02100 number of atom coordinates read : 4114 total number of charged atoms : 3964 net assigned charge : -1.499993 assigned positive charge : 624.8716 centred at (gu) : 91.59530 92.28802 100.1732 assigned negative charge : -626.3754 centred at (gu) : 91.73800 92.01955 100.2083 start vw surface at 0.2100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 77556 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41508 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 22952 mr = 50186 m= 2027 mr = 14682 m= 37 mr = 795 m= 0 mr = 1 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 36908 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 594 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 29663 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) : 0.5058542 object centre at (A) : 39.30600 74.40300 20.02100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4265552E-03 -1.8514276E-02 midg,1,midg; midg,igrid,midg -1.0724595E-02 1.0525903E-02 1,midg,midg; igrid,midg,midg 6.5453793E-03 -6.2079797E-03 gauss-seidel spectral radius is 0.9980165 estimated iterations to convergence 179 setup time was (sec) 1.030000 now iterating at: 14:10:09 rms-change max change #iterations 3.415377 150.0781 at 10iterations 1.364415 59.87085 at 20iterations 0.5443826 17.86689 at 30iterations 0.2183257 7.270761 at 40iterations 8.7440409E-02 3.206684 at 50iterations 3.4848318E-02 1.195214 at 60iterations 1.4027446E-02 0.4548903 at 70iterations 5.6311674E-03 0.2105319 at 80iterations 2.2728802E-03 7.7243805E-02 at 90iterations 9.2718983E-04 3.2875061E-02 at 100iterations 3.8434329E-04 1.3524592E-02 at 110iterations 1.6664380E-04 5.7864189E-03 at 120iterations finished qdiffx linear iterations at : 14:10:17 total time elapsed so far: 9.370000 # loops : 120 mean,max change (kT/e) : 1.6664380E-04 5.7864189E-03 energy calculations done at 9.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.550000 DelPhi exited at 14:10:18 9.554u 0.278s 0:10.19 96.3% 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 Mon Oct 10 2011 at 14:10:18 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 = 4114 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.276344 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): 4.118000 74.49400 ymin,ymax (A): 42.90300 105.9030 zmin,zma (A): -12.22500 52.26700 x,y,z range (A): 70.37601 63.00000 64.49200 scale (grids/A): 2.276344 object centre (A): 39.30600 74.40300 20.02100 number of atom coordinates read : 4114 total number of charged atoms : 3964 net assigned charge : -1.499993 assigned positive charge : 624.8716 centred at (gu) : 92.39265 93.43148 105.2595 assigned negative charge : -626.3754 centred at (gu) : 92.60696 93.02921 105.3122 start vw surface at 0.2000000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 180469 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41508 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 80409 mr = 124152 m= 21107 mr = 60992 m= 2883 mr = 14857 m= 126 mr = 1660 m= 5 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.740000 number of dielectric boundary points 83300 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 31621 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) : 1.517563 object centre at (A) : 39.30600 74.40300 20.02100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1286853 -0.5558021 midg,1,midg; midg,igrid,midg -0.1745744 0.2010323 1,midg,midg; igrid,midg,midg 0.1385991 -7.8477979E-02 gauss-seidel spectral radius is 0.9991165 estimated iterations to convergence 266 setup time was (sec) 2.080000 now iterating at: 14:10:20 rms-change max change #iterations 9.399516 287.2707 at 10iterations 5.361639 143.3928 at 20iterations 3.025225 72.61385 at 30iterations 1.691964 37.29037 at 40iterations 0.9437833 21.95231 at 50iterations 0.5234586 11.33500 at 60iterations 0.2894511 6.328838 at 70iterations 0.1599192 3.307186 at 80iterations 8.7977670E-02 2.028503 at 90iterations 4.8562545E-02 1.053185 at 100iterations 2.6655788E-02 0.5611525 at 110iterations 1.4617543E-02 0.3002949 at 120iterations 8.0283443E-03 0.1659870 at 130iterations 4.4136881E-03 9.0046406E-02 at 140iterations 2.4291205E-03 4.7763824E-02 at 150iterations 1.3387192E-03 2.8316498E-02 at 160iterations 7.4454455E-04 1.5368819E-02 at 170iterations 4.1885988E-04 8.3541870E-03 at 180iterations finished qdiffx linear iterations at : 14:10:34 total time elapsed so far: 15.88000 # loops : 180 mean,max change (kT/e) : 4.1885988E-04 8.3541870E-03 energy calculations done at 15.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.05000 DelPhi exited at 14:10:35 16.052u 0.311s 0:16.74 97.7% 0+0k 0+0io 0pf+0w