Sun Oct 9 08:10:28 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 Sun Oct 9 2011 at 08:10:28 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3094 !!! WARNING: NDP 1031 has a net charge of -2.1790 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: 0.5592911 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): 6.630000 54.83700 ymin,ymax (A): -30.89200 32.76000 zmin,zma (A): 124.6320 177.6080 x,y,z range (A): 48.20700 63.65200 52.97599 scale (grids/A): 0.5592911 object centre (A): 30.73350 0.9339991 151.1200 number of atom coordinates read : 3094 total number of charged atoms : 2955 net assigned charge : 8.321023 assigned positive charge : 461.2473 centred at (gu) : 90.84975 89.70847 89.15807 assigned negative charge : -452.9273 centred at (gu) : 90.84389 89.60258 89.19199 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6379 nv = 96 ne = 84 npr = 62538 no. pairs analyzed = 62538 no. exposed pairs = 3845 no. arc points = 27614 no. surface atoms = 1284 nbur = 1810 mkacc time = 0.1800000 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 = 1.512000 m= 279 mr = 3333 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.3900000 number of dielectric boundary points 3316 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2702 ## 286 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8156 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5080107E-09 4.0275125E-10 midg,1,midg; midg,igrid,midg -3.4547507E-10 1.8741841E-09 1,midg,midg; igrid,midg,midg 6.5387867E-10 1.1317954E-09 gauss-seidel spectral radius is 0.9835207 estimated iterations to convergence 64 setup time was (sec) 0.6500000 now iterating at: 08:10:29 rms-change max change #iterations 8.5843749E-02 12.77547 at 10iterations 6.2060733E-03 1.069969 at 20iterations 5.2563450E-04 8.4571838E-02 at 30iterations 9.0432310E-05 1.2180328E-02 at 40iterations 2.3627543E-05 3.2525063E-03 at 50iterations finished qdiffx linear iterations at : 08:10:32 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 2.3627543E-05 3.2525063E-03 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 08:10:33 4.109u 0.266s 0:04.64 93.9% 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 Sun Oct 9 2011 at 08:10:33 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3094 !!! WARNING: NDP 1031 has a net charge of -2.1790 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: 1.677873 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): 6.630000 54.83700 ymin,ymax (A): -30.89200 32.76000 zmin,zma (A): 124.6320 177.6080 x,y,z range (A): 48.20700 63.65200 52.97599 scale (grids/A): 1.677873 object centre (A): 30.73350 0.9339991 151.1200 number of atom coordinates read : 3094 total number of charged atoms : 2955 net assigned charge : 8.321023 assigned positive charge : 461.2473 centred at (gu) : 92.54881 89.12492 87.47390 assigned negative charge : -452.9273 centred at (gu) : 92.53151 88.80772 87.57580 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 69961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27614 grid for indexing accessible points = 1.400000 m= 22042 mr = 47598 m= 2443 mr = 15006 m= 69 mr = 1152 m= 0 mr = 7 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 550 time to turn everything in is 0.6200000 number of dielectric boundary points 30752 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 232 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 22776 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) : 0.5592911 object centre at (A) : 30.73350 0.9339991 151.1200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3290812E-03 1.9322913E-03 midg,1,midg; midg,igrid,midg 1.1859205E-02 2.6528874E-02 1,midg,midg; igrid,midg,midg 4.8424867E-03 1.0920573E-02 gauss-seidel spectral radius is 0.9983045 estimated iterations to convergence 193 setup time was (sec) 0.9400000 now iterating at: 08:10:34 rms-change max change #iterations 3.603156 156.5397 at 10iterations 1.541214 56.02039 at 20iterations 0.6623722 22.10772 at 30iterations 0.2846817 10.19271 at 40iterations 0.1225551 4.096638 at 50iterations 5.2549489E-02 1.821016 at 60iterations 2.2534549E-02 0.8190536 at 70iterations 9.7341044E-03 0.3376250 at 80iterations 4.1883197E-03 0.1416206 at 90iterations 1.8101011E-03 6.7588806E-02 at 100iterations 7.8674796E-04 2.5840759E-02 at 110iterations 3.4325290E-04 1.0925293E-02 at 120iterations finished qdiffx linear iterations at : 08:10:42 total time elapsed so far: 9.200000 # loops : 120 mean,max change (kT/e) : 3.4325290E-04 1.0925293E-02 energy calculations done at 9.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.360000 DelPhi exited at 08:10:43 9.364u 0.287s 0:09.99 96.4% 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 Sun Oct 9 2011 at 08:10:43 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3094 !!! WARNING: NDP 1031 has a net charge of -2.1790 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: 2.516810 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): 6.630000 54.83700 ymin,ymax (A): -30.89200 32.76000 zmin,zma (A): 124.6320 177.6080 x,y,z range (A): 48.20700 63.65200 52.97599 scale (grids/A): 2.516810 object centre (A): 30.73350 0.9339991 151.1200 number of atom coordinates read : 3094 total number of charged atoms : 2955 net assigned charge : 8.321023 assigned positive charge : 461.2473 centred at (gu) : 93.82280 88.68717 86.21057 assigned negative charge : -452.9273 centred at (gu) : 93.79715 88.21154 86.36358 start vw surface at 0.1700000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 162880 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27614 grid for indexing accessible points = 1.400000 m= 74538 mr = 116782 m= 22316 mr = 58400 m= 3821 mr = 16793 m= 258 mr = 2393 m= 7 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 1955 time to turn everything in is 1.520000 number of dielectric boundary points 69344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 23619 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) : 1.677873 object centre at (A) : 30.73350 0.9339991 151.1200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5817380E-02 1.5758522E-02 midg,1,midg; midg,igrid,midg -2.5613908E-02 0.3596418 1,midg,midg; igrid,midg,midg 5.0272003E-02 0.1581676 gauss-seidel spectral radius is 0.9991782 estimated iterations to convergence 275 setup time was (sec) 1.840000 now iterating at: 08:10:45 rms-change max change #iterations 9.203796 305.8486 at 10iterations 5.263500 128.2165 at 20iterations 3.008577 70.82962 at 30iterations 1.706233 41.63142 at 40iterations 0.9632370 23.12821 at 50iterations 0.5428537 11.50026 at 60iterations 0.3058439 6.542916 at 70iterations 0.1716093 4.008767 at 80iterations 9.6513897E-02 2.533912 at 90iterations 5.4008994E-02 1.309361 at 100iterations 3.0244324E-02 0.7471085 at 110iterations 1.6919063E-02 0.3562546 at 120iterations 9.4689103E-03 0.1898537 at 130iterations 5.2966150E-03 0.1074203 at 140iterations 2.9587138E-03 6.2839508E-02 at 150iterations 1.6539810E-03 3.4677505E-02 at 160iterations 9.2303660E-04 1.9123077E-02 at 170iterations 5.1653921E-04 9.9582672E-03 at 180iterations finished qdiffx linear iterations at : 08:10:58 total time elapsed so far: 15.39000 # loops : 180 mean,max change (kT/e) : 5.1653921E-04 9.9582672E-03 energy calculations done at 15.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.57000 DelPhi exited at 08:10:59 15.570u 0.298s 0:16.37 96.8% 0+0k 0+0io 0pf+0w