Mon Oct 10 14:24:46 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 14:24:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3060 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: 0.4795323 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): -15.74700 36.44500 ymin,ymax (A): -13.36200 60.87700 zmin,zma (A): 19.09600 76.69901 x,y,z range (A): 52.19200 74.23900 57.60300 scale (grids/A): 0.4795323 object centre (A): 10.34900 23.75750 47.89750 number of atom coordinates read : 3060 total number of charged atoms : 2911 net assigned charge : -0.4999888 assigned positive charge : 454.4702 centred at (gu) : 90.10767 90.93996 91.90524 assigned negative charge : -454.9713 centred at (gu) : 90.03795 91.02137 91.87392 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4543 nv = 96 ne = 84 npr = 59000 no. pairs analyzed = 59000 no. exposed pairs = 4405 no. arc points = 31572 no. surface atoms = 1455 nbur = 1605 mkacc time = 0.1300000 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 = 1.764000 m= 181 mr = 1970 m= 0 mr = 2 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2752 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3002 ## 581 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6193 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.2934944E-12 1.8891735E-11 midg,1,midg; midg,igrid,midg 2.3467605E-11 -4.5017490E-11 1,midg,midg; igrid,midg,midg -2.8788473E-11 2.6838632E-11 gauss-seidel spectral radius is 0.9776770 estimated iterations to convergence 56 setup time was (sec) 0.5200000 now iterating at: 14:24:46 rms-change max change #iterations 3.7028674E-02 8.223167 at 10iterations 1.7196859E-03 0.3283634 at 20iterations 8.4331441E-05 2.0057678E-02 at 30iterations 5.9261051E-06 1.7719269E-03 at 40iterations 6.9170994E-07 2.2125244E-04 at 50iterations finished qdiffx linear iterations at : 14:24:49 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 6.9170994E-07 2.2125244E-04 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 14:24:50 3.122u 0.144s 0:03.81 85.5% 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 14:24:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3060 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: 1.438597 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): -15.74700 36.44500 ymin,ymax (A): -13.36200 60.87700 zmin,zma (A): 19.09600 76.69901 x,y,z range (A): 52.19200 74.23900 57.60300 scale (grids/A): 1.438597 object centre (A): 10.34900 23.75750 47.89750 number of atom coordinates read : 3060 total number of charged atoms : 2911 net assigned charge : -0.4999888 assigned positive charge : 454.4702 centred at (gu) : 90.32231 92.81929 95.71494 assigned negative charge : -454.9713 centred at (gu) : 90.11371 93.06389 95.62160 start vw surface at 0.1600000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 50936 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31572 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 12496 mr = 31133 m= 846 mr = 7222 m= 11 mr = 242 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 273 time to turn everything in is 0.3900000 number of dielectric boundary points 25693 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 491 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 21444 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) : 0.4795323 object centre at (A) : 10.34900 23.75750 47.89750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6275255E-03 1.4640276E-03 midg,1,midg; midg,igrid,midg 1.2012089E-03 -1.0892959E-02 1,midg,midg; igrid,midg,midg -1.9245485E-03 4.5897588E-03 gauss-seidel spectral radius is 0.9976560 estimated iterations to convergence 164 setup time was (sec) 0.6500000 now iterating at: 14:24:50 rms-change max change #iterations 2.475519 140.9207 at 10iterations 0.9087046 52.82261 at 20iterations 0.3352918 15.93679 at 30iterations 0.1240274 5.491082 at 40iterations 4.5623705E-02 1.898726 at 50iterations 1.6865036E-02 0.7120205 at 60iterations 6.2201526E-03 0.2653415 at 70iterations 2.3059924E-03 0.1039200 at 80iterations 8.5689669E-04 3.4148678E-02 at 90iterations 3.1644103E-04 1.4225006E-02 at 100iterations 1.1680930E-04 4.7211647E-03 at 110iterations 4.3407876E-05 2.0203590E-03 at 120iterations finished qdiffx linear iterations at : 14:24:57 total time elapsed so far: 6.710000 # loops : 120 mean,max change (kT/e) : 4.3407876E-05 2.0203590E-03 energy calculations done at 6.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.900000 DelPhi exited at 14:24:57 6.899u 0.174s 0:07.82 90.2% 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 14:24:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3060 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: 2.157896 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): -15.74700 36.44500 ymin,ymax (A): -13.36200 60.87700 zmin,zma (A): 19.09600 76.69901 x,y,z range (A): 52.19200 74.23900 57.60300 scale (grids/A): 2.157896 object centre (A): 10.34900 23.75750 47.89750 number of atom coordinates read : 3060 total number of charged atoms : 2911 net assigned charge : -0.4999888 assigned positive charge : 454.4702 centred at (gu) : 90.48336 94.22874 98.57222 assigned negative charge : -454.9713 centred at (gu) : 90.17056 94.59568 98.43235 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 118766 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31572 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 46128 mr = 77973 m= 9776 mr = 33114 m= 1049 mr = 6181 m= 34 mr = 491 m= 3 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 809 time to turn everything in is 0.8500000 number of dielectric boundary points 57994 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 75 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 23160 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) : 1.438597 object centre at (A) : 10.34900 23.75750 47.89750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4742799E-02 3.4637850E-02 midg,1,midg; midg,igrid,midg 3.8838096E-02 -0.2122764 1,midg,midg; igrid,midg,midg -2.9635748E-02 8.0372095E-02 gauss-seidel spectral radius is 0.9989690 estimated iterations to convergence 246 setup time was (sec) 1.130000 now iterating at: 14:24:59 rms-change max change #iterations 7.140937 260.1132 at 10iterations 3.831943 115.2804 at 20iterations 2.038000 64.42462 at 30iterations 1.079117 30.89896 at 40iterations 0.5684785 20.25039 at 50iterations 0.2979421 7.304661 at 60iterations 0.1557103 4.055298 at 70iterations 8.1494749E-02 2.237595 at 80iterations 4.2426415E-02 1.096952 at 90iterations 2.2163741E-02 0.5733348 at 100iterations 1.1533783E-02 0.2940164 at 110iterations 5.9884456E-03 0.1439457 at 120iterations 3.1170666E-03 7.5890541E-02 at 130iterations 1.6178510E-03 4.6051025E-02 at 140iterations 8.3989050E-04 1.9636154E-02 at 150iterations 4.3611942E-04 1.2222290E-02 at 160iterations 2.2636843E-04 5.4817200E-03 at 170iterations 1.1752394E-04 2.8133392E-03 at 180iterations finished qdiffx linear iterations at : 14:25:08 total time elapsed so far: 10.53000 # loops : 180 mean,max change (kT/e) : 1.1752394E-04 2.8133392E-03 energy calculations done at 10.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.70000 DelPhi exited at 14:25:09 10.705u 0.167s 0:11.44 94.9% 0+0k 0+0io 0pf+0w