Mon Oct 10 17:02:12 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 17:02:12 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4312 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! 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= 0.1700000 grid size : 179 scale,in grids/A, set to be: 0.5147260 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): -16.04000 36.49900 ymin,ymax (A): -32.19100 31.28400 zmin,zma (A): -3.638000 65.52500 x,y,z range (A): 52.53900 63.47500 69.16300 scale (grids/A): 0.5147260 object centre (A): 10.22950 -0.4534988 30.94350 number of atom coordinates read : 4312 total number of charged atoms : 4106 net assigned charge : 0.8060333 assigned positive charge : 645.8803 centred at (gu) : 90.36162 90.74939 87.59567 assigned negative charge : -645.0782 centred at (gu) : 90.24770 90.80260 87.72112 start vw surface at 0.2700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 7152 nv = 96 ne = 84 npr = 88261 no. pairs analyzed = 88261 no. exposed pairs = 5591 no. arc points = 39015 no. surface atoms = 1864 nbur = 2448 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= 245 mr = 3582 m= 1 mr = 10 m= 0 mr = 0 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 3806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3765 ## 545 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 9631 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6134070E-10 -1.8550549E-10 midg,1,midg; midg,igrid,midg 1.2394778E-10 -1.7583507E-10 1,midg,midg; igrid,midg,midg -2.8683131E-10 3.4725528E-10 gauss-seidel spectral radius is 0.9806618 estimated iterations to convergence 59 setup time was (sec) 0.7200000 now iterating at: 17:02:13 rms-change max change #iterations 6.7321859E-02 10.55360 at 10iterations 3.8847562E-03 0.5600991 at 20iterations 2.7613677E-04 4.3865204E-02 at 30iterations 5.5266752E-05 7.0962906E-03 at 40iterations 1.7839975E-05 2.3123026E-03 at 50iterations finished qdiffx linear iterations at : 17:02:16 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 1.7839975E-05 2.3123026E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 17:02:17 3.523u 0.155s 0:04.31 85.1% 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 17:02:17 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4312 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! 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: 1.544178 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): -16.04000 36.49900 ymin,ymax (A): -32.19100 31.28400 zmin,zma (A): -3.638000 65.52500 x,y,z range (A): 52.53900 63.47500 69.16300 scale (grids/A): 1.544178 object centre (A): 10.22950 -0.4534988 30.94350 number of atom coordinates read : 4312 total number of charged atoms : 4106 net assigned charge : 0.8060333 assigned positive charge : 645.8803 centred at (gu) : 91.08394 92.24681 82.78561 assigned negative charge : -645.0782 centred at (gu) : 90.74276 92.40767 83.16307 start vw surface at 0.1900000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 80642 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39015 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 22622 mr = 54442 m= 1983 mr = 14601 m= 56 mr = 827 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 150 time to turn everything in is 0.5600000 number of dielectric boundary points 35433 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 497 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 30946 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) : 0.5147260 object centre at (A) : 10.22950 -0.4534988 30.94350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0334695E-03 -1.3854280E-02 midg,1,midg; midg,igrid,midg -1.2207658E-03 -6.9271624E-03 1,midg,midg; igrid,midg,midg -2.8214680E-03 9.0416800E-03 gauss-seidel spectral radius is 0.9980984 estimated iterations to convergence 182 setup time was (sec) 0.8300000 now iterating at: 17:02:18 rms-change max change #iterations 3.621146 159.8945 at 10iterations 1.472739 54.55468 at 20iterations 0.6010988 20.62449 at 30iterations 0.2465138 8.063231 at 40iterations 0.1002196 3.322743 at 50iterations 4.1153878E-02 1.467690 at 60iterations 1.6811809E-02 0.5514231 at 70iterations 6.8858732E-03 0.2395134 at 80iterations 2.8237221E-03 9.0423822E-02 at 90iterations 1.1601080E-03 4.0854454E-02 at 100iterations 4.7834482E-04 1.5209198E-02 at 110iterations 2.0015033E-04 6.6413879E-03 at 120iterations finished qdiffx linear iterations at : 17:02:24 total time elapsed so far: 7.270000 # loops : 120 mean,max change (kT/e) : 2.0015033E-04 6.6413879E-03 energy calculations done at 7.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 17:02:25 7.459u 0.219s 0:08.41 91.0% 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 17:02:25 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4312 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.316267 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): -16.04000 36.49900 ymin,ymax (A): -32.19100 31.28400 zmin,zma (A): -3.638000 65.52500 x,y,z range (A): 52.53900 63.47500 69.16300 scale (grids/A): 2.316267 object centre (A): 10.22950 -0.4534988 30.94350 number of atom coordinates read : 4312 total number of charged atoms : 4106 net assigned charge : 0.8060333 assigned positive charge : 645.8803 centred at (gu) : 91.62557 93.36971 79.17822 assigned negative charge : -645.0782 centred at (gu) : 91.11398 93.61133 79.74457 start vw surface at 0.1900000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 187672 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39015 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 81887 mr = 133989 m= 20137 mr = 63015 m= 2895 mr = 14007 m= 159 mr = 1747 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.7599999 no. cavity mid-points inaccessible to solvent = 544 time to turn everything in is 1.330000 number of dielectric boundary points 79948 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 32779 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) : 1.544178 object centre at (A) : 10.22950 -0.4534988 30.94350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1694899 -0.2829498 midg,1,midg; midg,igrid,midg -7.7579550E-02 -0.1836657 1,midg,midg; igrid,midg,midg -4.0598813E-02 0.1212923 gauss-seidel spectral radius is 0.9991497 estimated iterations to convergence 271 setup time was (sec) 1.610000 now iterating at: 17:02:27 rms-change max change #iterations 9.837312 316.2633 at 10iterations 5.614673 145.7425 at 20iterations 3.183483 69.85387 at 30iterations 1.794528 39.44686 at 40iterations 1.005706 23.08530 at 50iterations 0.5629798 12.13926 at 60iterations 0.3133275 6.555206 at 70iterations 0.1748310 3.931126 at 80iterations 9.7077325E-02 2.232844 at 90iterations 5.3884503E-02 1.138031 at 100iterations 2.9948896E-02 0.9054451 at 110iterations 1.6608989E-02 0.4289675 at 120iterations 9.2082024E-03 0.1979218 at 130iterations 5.1103998E-03 0.1013350 at 140iterations 2.8278744E-03 5.6182384E-02 at 150iterations 1.5687734E-03 3.0651093E-02 at 160iterations 8.7146269E-04 1.7277718E-02 at 170iterations 4.8698968E-04 8.9020729E-03 at 180iterations finished qdiffx linear iterations at : 17:02:37 total time elapsed so far: 11.41000 # loops : 180 mean,max change (kT/e) : 4.8698968E-04 8.9020729E-03 energy calculations done at 11.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.58000 DelPhi exited at 17:02:38 11.587u 0.219s 0:13.14 89.7% 0+0k 0+0io 0pf+0w