Mon Oct 10 11:11:36 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 11:11:36 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2128 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: 0.7461592 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): -21.60100 24.24100 ymin,ymax (A): -7.954000 38.61700 zmin,zma (A): -3.566000 44.14500 x,y,z range (A): 45.84200 46.57100 47.71100 scale (grids/A): 0.7461592 object centre (A): 1.320000 15.33150 20.28950 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.1439 centred at (gu) : 89.13530 89.69113 90.23627 assigned negative charge : -324.1440 centred at (gu) : 89.21038 89.72257 90.45131 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8171 nv = 96 ne = 84 npr = 43681 no. pairs analyzed = 43681 no. exposed pairs = 2723 no. arc points = 19449 no. surface atoms = 921 nbur = 1207 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 583 mr = 4498 m= 7 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 83 time to turn everything in is 0.2900000 number of dielectric boundary points 4152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1560 ## 137 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8548 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3829148E-07 -3.7239141E-07 midg,1,midg; midg,igrid,midg -6.7496956E-08 -1.2977178E-07 1,midg,midg; igrid,midg,midg -1.4918738E-08 -1.6096023E-07 gauss-seidel spectral radius is 0.9906431 estimated iterations to convergence 84 setup time was (sec) 0.6300000 now iterating at: 11:11:37 rms-change max change #iterations 0.2511013 34.42131 at 10iterations 3.3790201E-02 4.006936 at 20iterations 4.6406863E-03 0.5401268 at 30iterations 6.4341666E-04 7.6065063E-02 at 40iterations 8.7816174E-05 1.1169434E-02 at 50iterations finished qdiffx linear iterations at : 11:11:41 total time elapsed so far: 5.270000 # loops : 50 mean,max change (kT/e) : 8.7816174E-05 1.1169434E-02 energy calculations done at 5.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.450000 DelPhi exited at 11:11:42 5.455u 0.428s 0:06.14 95.6% 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 Mon Oct 10 2011 at 11:11:42 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2128 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: 2.238477 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): -21.60100 24.24100 ymin,ymax (A): -7.954000 38.61700 zmin,zma (A): -3.566000 44.14500 x,y,z range (A): 45.84200 46.57100 47.71100 scale (grids/A): 2.238477 object centre (A): 1.320000 15.33150 20.28950 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.1439 centred at (gu) : 87.40584 89.07341 90.70885 assigned negative charge : -324.1440 centred at (gu) : 87.63133 89.16776 91.35400 start vw surface at 0.1300000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 85924 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19449 grid for indexing accessible points = 1.400000 m= 33993 mr = 58853 m= 7136 mr = 25697 m= 732 mr = 4854 m= 19 mr = 371 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 2153 time to turn everything in is 0.7600000 number of dielectric boundary points 38029 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 15853 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) : 0.7461592 object centre at (A) : 1.320000 15.33150 20.28950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9981891E-03 -0.1475068 midg,1,midg; midg,igrid,midg -3.1396963E-02 -1.9454315E-02 1,midg,midg; igrid,midg,midg 1.1354301E-03 -3.2058402E-03 gauss-seidel spectral radius is 0.9989441 estimated iterations to convergence 243 setup time was (sec) 1.120000 now iterating at: 11:11:43 rms-change max change #iterations 5.192929 202.1116 at 10iterations 2.650083 97.06174 at 20iterations 1.356637 37.17377 at 30iterations 0.6958889 21.49308 at 40iterations 0.3559468 9.834780 at 50iterations 0.1822537 4.963494 at 60iterations 9.3158774E-02 2.581218 at 70iterations 4.7726493E-02 1.393460 at 80iterations 2.4462199E-02 0.7149019 at 90iterations 1.2567129E-02 0.3424482 at 100iterations 6.4503485E-03 0.1852379 at 110iterations 3.3103996E-03 8.8603973E-02 at 120iterations finished qdiffx linear iterations at : 11:11:55 total time elapsed so far: 12.83000 # loops : 120 mean,max change (kT/e) : 3.3103996E-03 8.8603973E-02 energy calculations done at 12.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 11:11:56 13.010u 0.491s 0:13.81 97.7% 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 11:11:56 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2128 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: 3.357716 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): -21.60100 24.24100 ymin,ymax (A): -7.954000 38.61700 zmin,zma (A): -3.566000 44.14500 x,y,z range (A): 45.84200 46.57100 47.71100 scale (grids/A): 3.357716 object centre (A): 1.320000 15.33150 20.28950 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.1439 centred at (gu) : 86.10881 88.61003 91.06329 assigned negative charge : -324.1440 centred at (gu) : 86.44704 88.75166 92.03104 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 197737 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19449 grid for indexing accessible points = 1.400000 m= 104996 mr = 142036 m= 44496 mr = 86821 m= 13609 mr = 36641 m= 2880 mr = 10580 m= 375 mr = 2066 m= 17 mr = 242 m= 0 mr = 0 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 6999 time to turn everything in is 2.330000 number of dielectric boundary points 85724 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.510000 number of grid points assigned charge 15912 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) : 2.238477 object centre at (A) : 1.320000 15.33150 20.28950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6983251E-02 -1.299215 midg,1,midg; midg,igrid,midg -0.3044475 -0.1113083 1,midg,midg; igrid,midg,midg 3.5663221E-02 -0.1339170 gauss-seidel spectral radius is 0.9993255 estimated iterations to convergence 304 setup time was (sec) 2.750000 now iterating at: 11:11:59 rms-change max change #iterations 11.15926 426.2175 at 10iterations 6.585924 122.7584 at 20iterations 3.893685 67.10461 at 30iterations 2.292721 42.55585 at 40iterations 1.355619 21.78297 at 50iterations 0.7987332 12.72135 at 60iterations 0.4696167 7.850040 at 70iterations 0.2769063 4.939527 at 80iterations 0.1628822 2.550652 at 90iterations 9.5980145E-02 1.588856 at 100iterations 5.6420334E-02 0.9464436 at 110iterations 3.3284534E-02 0.4914703 at 120iterations 1.9581614E-02 0.3185979 at 130iterations 1.1493553E-02 0.1840897 at 140iterations 6.7849807E-03 0.1034832 at 150iterations 3.9967070E-03 6.1082840E-02 at 160iterations 2.3549479E-03 3.9054871E-02 at 170iterations 1.3847953E-03 2.3841858E-02 at 180iterations finished qdiffx linear iterations at : 11:12:20 total time elapsed so far: 23.62000 # loops : 180 mean,max change (kT/e) : 1.3847953E-03 2.3841858E-02 energy calculations done at 23.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.79000 DelPhi exited at 11:12:20 23.790u 0.552s 0:24.63 98.8% 0+0k 0+0io 0pf+0w