Mon Oct 10 17:01:10 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+sph2.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 = amb2.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 17:01:10 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: 387 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4749 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: ZN8 822 has a net charge of 1.4000 !!! WARNING: FE 2 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5125989 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): -18.46700 36.44200 ymin,ymax (A): -30.27500 34.38100 zmin,zma (A): -4.080000 65.37000 x,y,z range (A): 54.90900 64.65600 69.45000 scale (grids/A): 0.5125989 object centre (A): 8.987501 2.053000 30.64500 number of atom coordinates read : 4749 total number of charged atoms : 4541 net assigned charge : 3.706028 assigned positive charge : 719.9474 centred at (gu) : 90.34385 90.37454 88.34258 assigned negative charge : -716.2458 centred at (gu) : 90.23589 90.38930 88.41315 start vw surface at 0.2500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 7820 nv = 96 ne = 84 npr = 96046 no. pairs analyzed = 96046 no. exposed pairs = 6063 no. arc points = 41594 no. surface atoms = 2028 nbur = 2721 mkacc time = 0.2000000 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 = 1.652000 m= 279 mr = 4018 m= 0 mr = 4 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 4077 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4080 ## 624 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 10514 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8936654E-10 -9.5105694E-11 midg,1,midg; midg,igrid,midg 8.5649030E-11 1.1898562E-11 1,midg,midg; igrid,midg,midg -2.3392335E-10 3.8710710E-10 gauss-seidel spectral radius is 0.9805328 estimated iterations to convergence 59 setup time was (sec) 0.7200000 now iterating at: 17:01:11 rms-change max change #iterations 7.0529081E-02 11.80719 at 10iterations 4.2913961E-03 0.6181335 at 20iterations 5.8715389E-04 7.6148033E-02 at 30iterations 1.9912394E-04 3.0484676E-02 at 40iterations 7.5246673E-05 1.2077332E-02 at 50iterations finished qdiffx linear iterations at : 17:01:13 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 7.5246673E-05 1.2077332E-02 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 17:01:14 3.486u 0.170s 0:04.54 80.3% 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 17:01:14 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: 387 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4749 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: ZN8 822 has a net charge of 1.4000 !!! WARNING: FE 2 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.537797 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): -18.46700 36.44200 ymin,ymax (A): -30.27500 34.38100 zmin,zma (A): -4.080000 65.37000 x,y,z range (A): 54.90900 64.65600 69.45000 scale (grids/A): 1.537797 object centre (A): 8.987501 2.053000 30.64500 number of atom coordinates read : 4749 total number of charged atoms : 4541 net assigned charge : 3.706028 assigned positive charge : 719.9474 centred at (gu) : 91.03009 91.12199 85.02619 assigned negative charge : -716.2458 centred at (gu) : 90.70755 91.16784 85.23925 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 88155 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41594 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25714 mr = 60122 m= 2224 mr = 16950 m= 41 mr = 931 m= 0 mr = 2 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.6100000 number of dielectric boundary points 38129 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 538 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 34219 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) : 0.5125989 object centre at (A) : 8.987501 2.053000 30.64500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6632765E-03 -7.0006573E-03 midg,1,midg; midg,igrid,midg 6.4236722E-03 -5.4204515E-03 1,midg,midg; igrid,midg,midg -1.6064219E-03 1.1281239E-02 gauss-seidel spectral radius is 0.9981250 estimated iterations to convergence 184 setup time was (sec) 0.8900000 now iterating at: 17:01:15 rms-change max change #iterations 3.857449 163.6137 at 10iterations 1.581763 53.22852 at 20iterations 0.6495824 20.77532 at 30iterations 0.2672589 9.216859 at 40iterations 0.1103469 3.559074 at 50iterations 4.5405537E-02 1.420561 at 60iterations 1.8680045E-02 0.5748901 at 70iterations 7.7652480E-03 0.2305260 at 80iterations 3.2546103E-03 0.1062779 at 90iterations 1.3955636E-03 4.2785645E-02 at 100iterations 6.3722860E-04 2.2217274E-02 at 110iterations 3.2714455E-04 1.1085510E-02 at 120iterations finished qdiffx linear iterations at : 17:01:22 total time elapsed so far: 7.210000 # loops : 120 mean,max change (kT/e) : 3.2714455E-04 1.1085510E-02 energy calculations done at 7.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.380000 DelPhi exited at 17:01:23 7.386u 0.206s 0:08.59 88.2% 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 Mon Oct 10 2011 at 17:01:23 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: 387 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4749 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: ZN8 822 has a net charge of 1.4000 !!! WARNING: FE 2 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= 0.2000000 grid size : 179 scale,in grids/A, set to be: 2.306695 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): -18.46700 36.44200 ymin,ymax (A): -30.27500 34.38100 zmin,zma (A): -4.080000 65.37000 x,y,z range (A): 54.90900 64.65600 69.45000 scale (grids/A): 2.306695 object centre (A): 8.987501 2.053000 30.64500 number of atom coordinates read : 4749 total number of charged atoms : 4541 net assigned charge : 3.706028 assigned positive charge : 719.9474 centred at (gu) : 91.54478 91.68282 82.53903 assigned negative charge : -716.2458 centred at (gu) : 91.06140 91.75148 82.85887 start vw surface at 0.2700000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 205883 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41594 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 91701 mr = 148377 m= 23093 mr = 71139 m= 3202 mr = 16466 m= 187 mr = 1887 m= 2 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 148 time to turn everything in is 1.510000 number of dielectric boundary points 86139 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 36234 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) : 1.537797 object centre at (A) : 8.987501 2.053000 30.64500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1825264 -0.1677278 midg,1,midg; midg,igrid,midg 0.1059518 -0.1489850 1,midg,midg; igrid,midg,midg -1.9440886E-02 0.1733247 gauss-seidel spectral radius is 0.9991657 estimated iterations to convergence 273 setup time was (sec) 1.800000 now iterating at: 17:01:25 rms-change max change #iterations 10.39543 318.3909 at 10iterations 5.979687 149.8561 at 20iterations 3.412999 90.05621 at 30iterations 1.927563 43.92591 at 40iterations 1.089143 23.00001 at 50iterations 0.6135477 12.04173 at 60iterations 0.3442058 7.334122 at 70iterations 0.1926602 4.022738 at 80iterations 0.1076761 2.192179 at 90iterations 6.0050335E-02 1.119211 at 100iterations 3.3515617E-02 0.7186953 at 110iterations 1.8726559E-02 0.3563452 at 120iterations 1.0424936E-02 0.2020531 at 130iterations 5.8120382E-03 0.1270885 at 140iterations 3.2398968E-03 7.3230743E-02 at 150iterations 1.8152252E-03 3.7143707E-02 at 160iterations 1.0202111E-03 1.8510818E-02 at 170iterations 5.7880575E-04 1.2516022E-02 at 180iterations finished qdiffx linear iterations at : 17:01:35 total time elapsed so far: 11.49000 # loops : 180 mean,max change (kT/e) : 5.7880575E-04 1.2516022E-02 energy calculations done at 11.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.69000 DelPhi exited at 17:01:36 11.695u 0.227s 0:13.33 89.3% 0+0k 0+0io 0pf+0w