Sat Oct 15 12:07:07 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 Sat Oct 15 2011 at 12:07:07 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3255 !!! WARNING: HIT 82 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 0.5929973 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): -16.73300 40.24000 ymin,ymax (A): 16.54700 76.58100 zmin,zma (A): 25.28500 83.34800 x,y,z range (A): 56.97300 60.03400 58.06300 scale (grids/A): 0.5929973 object centre (A): 11.75350 46.56400 54.31650 number of atom coordinates read : 3255 total number of charged atoms : 3113 net assigned charge : 10.97103 assigned positive charge : 484.7377 centred at (gu) : 90.21815 90.19769 91.90956 assigned negative charge : -473.7683 centred at (gu) : 90.09480 90.23083 92.10849 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7977 nv = 96 ne = 84 npr = 62914 no. pairs analyzed = 62914 no. exposed pairs = 4305 no. arc points = 31628 no. surface atoms = 1427 nbur = 1828 mkacc time = 0.1500000 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 = 1.456000 m= 371 mr = 4102 m= 3 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 4214 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3139 ## 333 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9809 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9959860E-09 -5.4412652E-09 midg,1,midg; midg,igrid,midg 4.8267235E-09 2.8059139E-09 1,midg,midg; igrid,midg,midg -5.4428123E-10 8.6178868E-09 gauss-seidel spectral radius is 0.9853562 estimated iterations to convergence 68 setup time was (sec) 0.6200000 now iterating at: 12:07:08 rms-change max change #iterations 0.1169753 15.79926 at 10iterations 9.5992181E-03 1.771618 at 20iterations 8.1393891E-04 0.1286681 at 30iterations 7.7249446E-05 9.6497536E-03 at 40iterations 1.0094353E-05 9.7656250E-04 at 50iterations finished qdiffx linear iterations at : 12:07:11 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 1.0094353E-05 9.7656250E-04 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 12:07:11 3.561u 0.189s 0:04.04 92.5% 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 Sat Oct 15 2011 at 12:07:11 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3255 !!! WARNING: HIT 82 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.778992 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): -16.73300 40.24000 ymin,ymax (A): 16.54700 76.58100 zmin,zma (A): 25.28500 83.34800 x,y,z range (A): 56.97300 60.03400 58.06300 scale (grids/A): 1.778992 object centre (A): 11.75350 46.56400 54.31650 number of atom coordinates read : 3255 total number of charged atoms : 3113 net assigned charge : 10.97103 assigned positive charge : 484.7377 centred at (gu) : 90.65379 90.59225 95.72791 assigned negative charge : -473.7683 centred at (gu) : 90.28418 90.69205 96.32516 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 86749 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31628 grid for indexing accessible points = 1.400000 m= 28982 mr = 58400 m= 3784 mr = 20315 m= 162 mr = 2055 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 463 time to turn everything in is 0.6400000 number of dielectric boundary points 38880 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 277 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 24268 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) : 0.5929973 object centre at (A) : 11.75350 46.56400 54.31650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3099757E-02 1.8417324E-03 midg,1,midg; midg,igrid,midg 4.1466236E-02 2.0522051E-02 1,midg,midg; igrid,midg,midg -8.8818045E-03 1.7149208E-02 gauss-seidel spectral radius is 0.9985245 estimated iterations to convergence 206 setup time was (sec) 0.9400000 now iterating at: 12:07:12 rms-change max change #iterations 4.209439 215.5021 at 10iterations 1.901420 64.00307 at 20iterations 0.8635970 30.30080 at 30iterations 0.3901496 11.06867 at 40iterations 0.1772865 5.835419 at 50iterations 8.0303900E-02 2.396191 at 60iterations 3.6401972E-02 1.168007 at 70iterations 1.6564026E-02 0.4855461 at 80iterations 7.4830698E-03 0.2377951 at 90iterations 3.4113694E-03 0.1072102 at 100iterations 1.5501416E-03 5.2901268E-02 at 110iterations 7.0560107E-04 2.2511482E-02 at 120iterations finished qdiffx linear iterations at : 12:07:19 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 7.0560107E-04 2.2511482E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 12:07:20 7.982u 0.278s 0:08.69 94.9% 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 Sat Oct 15 2011 at 12:07:20 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3255 !!! WARNING: HIT 82 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 2.668488 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): -16.73300 40.24000 ymin,ymax (A): 16.54700 76.58100 zmin,zma (A): 25.28500 83.34800 x,y,z range (A): 56.97300 60.03400 58.06300 scale (grids/A): 2.668488 object centre (A): 11.75350 46.56400 54.31650 number of atom coordinates read : 3255 total number of charged atoms : 3113 net assigned charge : 10.97103 assigned positive charge : 484.7377 centred at (gu) : 90.98051 90.88807 98.59200 assigned negative charge : -473.7683 centred at (gu) : 90.42629 91.03815 99.48773 start vw surface at 0.1700000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 200933 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31628 grid for indexing accessible points = 1.400000 m= 96442 mr = 142599 m= 31279 mr = 76526 m= 6372 mr = 23978 m= 653 mr = 4387 m= 15 mr = 349 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 1558 time to turn everything in is 1.610000 number of dielectric boundary points 87855 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 24892 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) : 1.778992 object centre at (A) : 11.75350 46.56400 54.31650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6238855 1.4024546E-02 midg,1,midg; midg,igrid,midg 0.5868058 0.4626452 1,midg,midg; igrid,midg,midg -5.8021840E-02 0.2060147 gauss-seidel spectral radius is 0.9992594 estimated iterations to convergence 290 setup time was (sec) 1.950000 now iterating at: 12:07:22 rms-change max change #iterations 10.38203 324.7152 at 10iterations 6.117768 150.7146 at 20iterations 3.583808 78.31137 at 30iterations 2.082478 47.49300 at 40iterations 1.212293 24.84390 at 50iterations 0.7028357 16.27938 at 60iterations 0.4051626 7.617699 at 70iterations 0.2338521 4.289871 at 80iterations 0.1348850 2.844814 at 90iterations 7.7682026E-02 1.430197 at 100iterations 4.4623096E-02 0.7953720 at 110iterations 2.5711093E-02 0.4553165 at 120iterations 1.4774698E-02 0.2827129 at 130iterations 8.4826518E-03 0.1458817 at 140iterations 4.8824116E-03 8.1420898E-02 at 150iterations 2.8050996E-03 5.2608490E-02 at 160iterations 1.6101369E-03 2.7096152E-02 at 170iterations 9.2453818E-04 1.6222954E-02 at 180iterations finished qdiffx linear iterations at : 12:07:33 total time elapsed so far: 13.03000 # loops : 180 mean,max change (kT/e) : 9.2453818E-04 1.6222954E-02 energy calculations done at 13.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.21000 DelPhi exited at 12:07:34 13.214u 0.263s 0:13.79 97.6% 0+0k 0+0io 0pf+0w