Sat Oct 15 14:11:56 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 Sat Oct 15 2011 at 14:11:57 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5236 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5050720 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): -18.89600 36.57300 ymin,ymax (A): -30.63700 32.45000 zmin,zma (A): -4.127000 66.35800 x,y,z range (A): 55.46900 63.08700 70.48500 scale (grids/A): 0.5050720 object centre (A): 8.838501 0.9064999 31.11550 number of atom coordinates read : 5236 total number of charged atoms : 4984 net assigned charge : 6.800036 assigned positive charge : 787.4423 centred at (gu) : 90.63815 90.72790 89.44769 assigned negative charge : -780.6476 centred at (gu) : 90.55708 90.75182 89.43555 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8305 nv = 96 ne = 84 npr = 106716 no. pairs analyzed = 106716 no. exposed pairs = 6510 no. arc points = 44661 no. surface atoms = 2210 nbur = 3026 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 = 1.680000 m= 310 mr = 4310 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 4303 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4403 ## 721 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 11260 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4448134E-11 8.7914051E-11 midg,1,midg; midg,igrid,midg 1.0551133E-10 2.4716106E-11 1,midg,midg; igrid,midg,midg -9.0818839E-11 3.0068459E-10 gauss-seidel spectral radius is 0.9799831 estimated iterations to convergence 58 setup time was (sec) 0.5600000 now iterating at: 14:12:01 rms-change max change #iterations 6.8410322E-02 10.47338 at 10iterations 4.5621577E-03 0.6908607 at 20iterations 8.5196388E-04 0.1091614 at 30iterations 3.0883824E-04 3.7149429E-02 at 40iterations 1.2184282E-04 1.5821457E-02 at 50iterations finished qdiffx linear iterations at : 14:12:11 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 1.2184282E-04 1.5821457E-02 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 14:12:13 4.213u 0.235s 0:15.71 28.2% 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 Sat Oct 15 2011 at 14:12:13 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5236 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.515216 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): -18.89600 36.57300 ymin,ymax (A): -30.63700 32.45000 zmin,zma (A): -4.127000 66.35800 x,y,z range (A): 55.46900 63.08700 70.48500 scale (grids/A): 1.515216 object centre (A): 8.838501 0.9064999 31.11550 number of atom coordinates read : 5236 total number of charged atoms : 4984 net assigned charge : 6.800036 assigned positive charge : 787.4423 centred at (gu) : 91.91301 92.18210 88.34140 assigned negative charge : -780.6476 centred at (gu) : 91.67095 92.25531 88.30615 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 95385 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44661 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 26858 mr = 66059 m= 2415 mr = 17476 m= 67 mr = 972 m= 0 mr = 2 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 40216 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 653 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 37364 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) : 0.5050720 object centre at (A) : 8.838501 0.9064999 31.11550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8093573E-03 1.6535118E-02 midg,1,midg; midg,igrid,midg -1.4471430E-03 -1.1002972E-02 1,midg,midg; igrid,midg,midg -1.0126590E-03 1.0722873E-02 gauss-seidel spectral radius is 0.9981043 estimated iterations to convergence 183 setup time was (sec) 0.7700000 now iterating at: 14:12:14 rms-change max change #iterations 3.908792 157.9594 at 10iterations 1.596518 53.50372 at 20iterations 0.6534983 20.79285 at 30iterations 0.2685053 8.799924 at 40iterations 0.1099157 3.608410 at 50iterations 4.5243710E-02 1.401361 at 60iterations 1.8574471E-02 0.5841541 at 70iterations 7.6876599E-03 0.2424011 at 80iterations 3.2689916E-03 0.1032410 at 90iterations 1.4507604E-03 4.4860125E-02 at 100iterations 7.2553678E-04 2.3876190E-02 at 110iterations 4.1700414E-04 1.2574673E-02 at 120iterations finished qdiffx linear iterations at : 14:12:32 total time elapsed so far: 9.010000 # loops : 120 mean,max change (kT/e) : 4.1700414E-04 1.2574673E-02 energy calculations done at 9.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.140000 DelPhi exited at 14:12:32 9.141u 0.302s 0:19.38 48.7% 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 Sat Oct 15 2011 at 14:12:32 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5236 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.272824 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): -18.89600 36.57300 ymin,ymax (A): -30.63700 32.45000 zmin,zma (A): -4.127000 66.35800 x,y,z range (A): 55.46900 63.08700 70.48500 scale (grids/A): 2.272824 object centre (A): 8.838501 0.9064999 31.11550 number of atom coordinates read : 5236 total number of charged atoms : 4984 net assigned charge : 6.800036 assigned positive charge : 787.4423 centred at (gu) : 92.86906 93.27287 87.51176 assigned negative charge : -780.6476 centred at (gu) : 92.50621 93.38279 87.45919 start vw surface at 0.1200000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 222976 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44661 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 97031 mr = 162867 m= 23605 mr = 75022 m= 3392 mr = 16448 m= 178 mr = 2010 m= 0 mr = 54 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.160000 number of dielectric boundary points 90781 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 82 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 39742 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) : 1.515216 object centre at (A) : 8.838501 0.9064999 31.11550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1240933 0.3127319 midg,1,midg; midg,igrid,midg -0.1113361 -0.2610066 1,midg,midg; igrid,midg,midg -1.1863973E-02 0.1709722 gauss-seidel spectral radius is 0.9991695 estimated iterations to convergence 274 setup time was (sec) 1.470000 now iterating at: 14:12:38 rms-change max change #iterations 10.62444 349.7170 at 10iterations 6.111300 133.5931 at 20iterations 3.480662 90.64870 at 30iterations 1.971870 41.37010 at 40iterations 1.113112 28.11535 at 50iterations 0.6258401 13.24443 at 60iterations 0.3524714 8.015522 at 70iterations 0.1973890 3.794355 at 80iterations 0.1105305 2.120445 at 90iterations 6.1760023E-02 1.178345 at 100iterations 3.4574483E-02 0.6731873 at 110iterations 1.9263420E-02 0.3623848 at 120iterations 1.0763026E-02 0.1976080 at 130iterations 6.0201194E-03 0.1255386 at 140iterations 3.3646040E-03 6.5776825E-02 at 150iterations 1.8887632E-03 3.8864136E-02 at 160iterations 1.0683323E-03 2.2791147E-02 at 170iterations 6.1292236E-04 1.1733055E-02 at 180iterations finished qdiffx linear iterations at : 14:13:04 total time elapsed so far: 14.53000 # loops : 180 mean,max change (kT/e) : 6.1292236E-04 1.1733055E-02 energy calculations done at 14.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.67000 DelPhi exited at 14:13:05 14.671u 0.297s 0:32.14 46.5% 0+0k 0+0io 0pf+0w